Police said Roy's body was recovered from a bush beside the highway, two kilometres from Dadpur. He was taken to Chuchura Imambara hospital, where he was declared brought dead.
"There are two external injury marks on Roy's throat and eye. Post mortem report said he was killed by strangulation," police said.
They said they are investigating what he was doing in Hoogly and who killed him.
The Trinamool termed the murder as a "political killing" and alleged that the BJP was involved.
"He was a young leader and an active member of our party. He certainly had political enemies. The miscreants, who used to torture people here during the Left Front regime, have now joined the BJP. Police should thoroughly investigate the matter," state Transport Minister Subhendu Adhikari alleged.
"We have full faith in police. The family members have already lodged an FIR. His death is a loss for our party," he said.
Family members said they last heard from Roy on February 7 when he informed that he was in Hooghly district for some personal work.
"After we got the news from police in Hooghly, I went there and identified his body. We want strong action against the murderers," Roy's son said.
His death comes on the back of political blame game between Trinamool Congress and BJP over the brutal killing of MLA Satyajit Biswas, who was shot dead from point blank range by a group of unidentified assailants in Hooghly's Krishnagunj on Saturday night.
While the Trinamool accused BJP leader Mukul Roy and his associates of masterminding the killing, the saffron party refuted the charges and claimed that the leader was killed due to Trinamool's infighting.