At the start of Ewan Morrison's 2009 novel Ménage, one character of the book's threesome, Owen Morgan, introduces the art exhibition by his friend and former lover Dorothy Shears and implores us, the viewers, to lay aside all judgement, trust her, "close your eyes, and enter the darkness with her".

In Morrison's fourth novel, the appeal becomes both the title and something of an urgent refrain. But in Close Your Eyes, it is not the viewer-reader who is addressed, but the protagonist. Closing her eyes is vital for summoning up the past, imagining the future and blotting out the pain of the present. We enter a new and far more disorientating darkness with her. The result is Morrison's most accomplished book yet.

The novel follows post-natally depressed Rowan as she deserts her husband and baby daughter to unravel the secret of her mother's death 30 years ago. Sleep deprived, confused, but aware that her "mental map is all wrong", she drives north to Ithaca, a New-Age commune in Caithness where she spent the first 10 years of her life.

There, her mother, Jenna, shielded her from the "plastic people" of the outside world and instilled in her different values for an alternative way of living – that is, until Jenna became the black sheep of the flock for her increasing paranoia about the threat of a mushroom cloud from the nuclear stockpile down the road at Dounreay.

Jenna fled and died in a car crash, but Rowan has evidence that suggests she is still alive. Ignoring the frantic calls from her husband, and wrestling with the guilt of abandoning her child, Rowan's paper-chase turns into a thrilling hunt to unearth the truth which has been kept from her for decades.

Morrison expertly unpeels one narrative layer after another to enlighten Rowan and jolt the reader. Rowan is a beguiling creation. Where she was once feistily independent she is now "addicted to self-help", though enjoying the privileges of an expensive London apartment, an SUV and upwardly mobile friends. She even has a different identity – Emma – and has hidden from her husband all aspects of her former life.

When she revisits and infiltrates the revamped commune, the memories come flooding back, along with righteous anger, giving Morrison the opportunity to shade in her real past, including the colourful figures with whom she and her mother once cohabited.

Back-story routinely stalls or derails narrative momentum but Morrison knows exactly what he is doing, and his frequent jumps between present and past are neat segues. He switches deftly from the tumultuous thoughts and self-reproach that lace Rowan's perspective to that of Jenna, where he dazzles with a convincing second-person voice.

At times both mother and daughter are referred to as "she", with Morrison blending both characters, informing us that in a sense they are reflections of each other: a woman who has abandoned her daughter to embark on a private journey of self-discovery. In a lesser writer's hands this mirroring could have been too slick but Morrison creates a perfect symmetry. He consistently impresses when entering Rowan's mind and detailing her mother-love and maternal frustration, and there are six stunning pages in which Rowan recounts her hell in labour, from contractions to haemorrhaging.

Morrison seems to have grown up as a writer, and is certainly less afraid of taking risks. Life in the commune reads like an authentic first-hand account, right up to when Jenna sees her spiritual guru as a hypocrite and Rowan realises she has been raised not as a child but as "a metaphor - you were the future, the brave new world".

There is, however, the occasional slip-up. Other metaphors fall flat (Jenna gives birth and out pops Rowan "as perfect as a poem") and Eva, the wicked witch who "destroyed" Jenna, feels underwritten. The modern-day Ithaca is, perhaps inevitably, less interesting than its earlier incarnation, more happy-clappy than trippy-hippy, and is weakened further by Morrison's ragtag bunch of attendees. "We have some problems, jah?" says a Dutch girl, at once exposing the problem to be silly stereotyping. A girl with a "Phoney norf Lundun accent" says "Knowwhattamean?"

Morrison tries to pre-empt criticism of an American's speech by declaring "Tom is a stereotype. He must know this too, maybe that is his problem." The author's problem is that they all come across as stick-figure stereotypes and consequently don't ring true. Thankfully their appearance is fleeting and so they can't sully the richer-drawn characters that haunt Rowan's past.

Close Your Eyes marks a significant departure for Morrison. His first three sex-infused novels offered, at least superficially, what it said on the tin: Swung (2007) about swingers, Distance (2008) about long-distance love, Ménage (2009) about the heady antics of three housemates. He could have got a fourth novel on sex – what better than to explore the loose living and free love of a 60s and 70s hippy commune? – and indeed at one point there is brief mention of "a ménage of sorts" between two commune members.

But he judiciously pans out and changes topic, evincing a clear-cut been-there, done-that. What we get instead is a complex, thought-provoking and deeply ambitious book, and one that Morrison, now an exceedingly versatile writer, pulls off triumphantly.

Ewan Morrison is at the Edinburgh International Book Festival on August 11, 12 and 23.

For details go to www.edbookfest.co.uk, tel 0845 373 5888