Mr Darling will attend the gathering in Stirling to launch a new Better Together group, called Forces Together, to rally support from those who have served in the military.
But the unprecedented move – he is believed to be the first Labour MP to attend a Scots Tory conference –drew a scathing response from the SNP.
Nationalist MSP Annabelle Ewing said: "This is bad news for the No campaign. Many Labour voters will be appalled at the prospect of Alistair Darling going to the Tory conference to get his instructions.
"The reality is the No campaign is led by the Tory Government at Westminster, which the people of Scotland didn't vote for, and is inflicting cruel cuts on working families and vulnerable people. In attending the Tory conference, Mr Darling is proving the No campaign prefers bad Government from Westminster to good government with independence."
The Tory conference will hear keynote speeches from Prime Minister David Cameron as well as Scots leader Ruth Davidson.
Ms Davidson yesterday hit back at criticism of her leadership, saying "navel gazing" about her performances at Holyrood was a distraction from rebuilding the party.
Mr Cameron said he would use his speech to argue the UK needs to "pull together" in a global economic race.