In a stark assessment, the Paisley and Renfrewshire South MP said the debate had become "arid" and clashes over the country's future had become "infected" by personal insults.
Mr Alexander said that there was a danger the growing animosity between the two sides would not end after next year's referendum, leaving a damaging legacy for politics and civic life. His comments come in a speech to be delivered in his constituency tonight.
Mr Alexander will say: "Stepping back over the summer from the day to day exchanges confirmed to me just how arid much of the contemporary constitutional debate has become.
"In the last year alone we've seen a debate characterised all too often by shallowness, grievance and personal vitriol.
"There is a real risk that the vitriol, which at times has infected the debate, will not simply fade post 18th September 2014, and when people look beneath the surface of whatever numbers define the result, it will not be a pleasant view.
"Whatever the outcome of the vote, that cannot and would not be good for Scotland."
He said the referendum battle had overstepped a healthy "rigorous and passionate debate".
His warning echoes remarks by broadcaster Andrew Marr who complained about the "very, very aggressive" tone of the debate on both sides.
The BBC journalist told an Edinburgh International Book Festival audience in the summer: "It is wrong and dangerous because whatever happens next year you are all going to have to live together afterwards."
Mr Alexander will use his speech tonight to call on all parties, including the SNP, to sign up to a National Convention on Scotland's future in the event of a No vote.
He first raised the proposal in March when it met a positive reaction from Labour, Lib Dems and Tory MSPs.
He will say: "It would be both an expression of our patriotism and pride in Scotland, and a mechanism by which to translate our sense of possibility for post-2014 Scotland into practical policies.
"Indeed it would be a very tangible answer to the question 'What comes next if Scotland rejects separation in 2014?"
He will add: "All sides of this debate have an interest in the referendum outcome being respected.
"So if, in a year's time, Scotland does reject separation, then why shouldn't Nationalists too come to see a National Convention as a constructive means to discuss, deliberate and decide together on what our better future within the UK looks like?"
Mr Alexander said the National Convention should consider ways to develop devolution and increase Holyrood's powers.
But he insisted it should also look at ways of tackling long-term political challenges such as Scotland's ageing population. He will say: "All of us - myself included - seeking to improve the devolution settlement need the humility to acknowledge that the debate about 'powers for the parliament', just like the debate about separation, has too often in the past left the public cold."
Mr Marr, who also warned of a "toxic" anti-English element to the independence debate, was strongly criticised by the SNP.
At the time the party said it was "disappointed with the picture of Scotland he painted".