The 30-year-old crewman got caught in the netting mechanism on board the vessel Ocean Spray, which was 14 miles off Newlyn.
It is understood that the net slammed him against the side of the vessel and he was flipped overboard.
The crewman has been taken to the Royal Cornwall Hospital in Treliske with injuries to his legs and waist.
Coastguards spokesman said an 8ft swell made it too difficult for the sailor to be transferred to a helicopter or a lifeboat during the incident on Wednesday night.
The Penlee lifeboat escorted the vessel to shore and the sailor was then taken to hospital by land ambulance.
article copyright THE CORNISHMAN