Chief executive Dalton Philips wants to remove layers of management that currently mean some stores have seven tiers between the shop floor and the store manager.
The changes will involve around 2,600 redundancies, although Morrisons said this year will also see it create 1,000 jobs in its M local convenience stores and an additional 3,000 in new supermarkets.
It said it will look to relocate staff to these businesses where possible.
The new store structure will bring together department managers and supervisor positions into a single and smaller tier of team managers.
From this group Morrisons is proposing to promote 1,000 into new duty manager roles to strengthen the senior management team in each store. Hours will also be re-invested in customer-facing jobs on the shop floor.
Mr Philips said: "This is the right time to modernise the way our stores are managed. These changes will improve our focus on customers and lead to simpler, smarter ways of working.
"We know that moving to the new management structure will mean uncertainty for our colleagues and we will be supporting them through the process."
The company said a trial of the new management structure found that it led to stronger performance and clearer lines of responsibility. It added that more staff were in roles where they can engage with customers.
The changes come amid increasing pressure on Mr Philips after the Bradford-based chain racked up an annual loss of £176 million in the year to February and recently announced a 7.1% decline in quarterly sales.
The poor performance led to a humiliating public dressing down by former chairman Sir Ken Morrison at the supermarket's AGM earlier this month.
Sir Ken, who retired in 2008 after 55 years in which the company became the UK's fourth biggest grocer, reportedly described Mr Philips's strategy as ''bullshit''.
Mr Philips has previously made stark comments about the need to drag the supermarket into the 21st century, though he has refrained from criticising his predecessors.
As well as investing £1 billion in price cuts over three years, he has launched an online operation, expanded Morrisons' presence in the convenience store sector and moved to update antiquated IT systems.
Morrisons said it had today opened discussions with staff and their representatives about the new management structure.
The chain, which employs more than 126,000 staff, has 511 supermarkets and 117 convenience stores.