The former Norwich City player poached the opener with a close-range tap-in after 34 minutes, but his other two goals were quality finishes.
With County still pushing for an equaliser, Thorne stylishly converted Paul Evans' corner with a low right-foot volley just before the hour mark and capped a man-of-the-match display with a fierce drive in the final minute.
The Magpies were pegged back from the start as City went looking for back-to-back wins and keeper Kevin Pilkington made two excellent saves early on.
After 12 minutes Pilkington saved a near-post shot from Thorne with his legs and six minutes later got down smartly to stop a low drive from winger Omar Daley.
But the former Manchester United keeper was at fault when he failed to reach Evans' 34th-minute corner and, after David Wetherall's header was cleared off the line, the loose ball fell at the feet of Thorne who poked it home from a yard out.
County rarely tested City's back-line, but keeper Donovan Ricketts was relieved to block an angled shot from Lawrie Dudfield after half-an-hour.
Two minutes before the break Thorne sent strike partner Barry Conlon bursting clear, but his shot was superbly saved by Pilkington and Lee Canoville got back to clear the danger.
The Magpies, who have now won just one game in 11, put on some pressure after the interval but Ricketts did well to grab a loose ball in the box as Dudfield threatened.
Thorne bagged his second from a well-worked corner and his clinical finish knocked the stuffing out of the visitors.
The Magpies failed to make the most of a series of free-kicks late on, but they were caught by a sucker-punch when Thorne drilled in his hat-trick goal.
The striker raced onto a neat pass from winger Joe Colbeck and fired in his third with a fierce 20-yard right-foot finish.