The deceased was identified as Motin Mia, 40, son of Nur Uddin of Burideao village in the upazila.
The accident took place on Sylhet-Bholaganj Highway when the bus collided with the auto-rickshaw around 6am, leaving Motin critically injured, said Sajal Kumar Kanu, officer-in-charge of Companiganj Police Station.
Later, he was taken to Companiganj Health Complex where doctors declared him dead.
After the accident, locals and other auto-rickshaw drivers blocked the Sylhet-Bholaganj Highway, halting the vehicular movement.
Later, they withdrew the blockade after Upazila Nirbahi Officer Sumon Acharya promised to take necessary steps in this connection.
Police recovered the body and sent it to Syllhet MAG Medical College Hospital morgue for autopsy, the OC added.