The 23-year-old Garmin-Transitions rider's lone attack on the densely wooded five-kilometre climb of Ustron in the fifth stage earned him a 20-second advantage at the summit over Slovenia's Grega Bole, with Poland's Sylvester Szmyd in third.
With two stages remaining, Martin leads by 14 seconds overall ahead of Bole. Italy's Alessandro Ballan is third, 21 seconds back.
The nephew of 1987 Tour de France winner Stephen Roche, Martin said driving out to inspect the stage finish on Thursday morning had provided key information for the first ProTour victory and lead of his career.
"We found there was a tough cobbled section about halfway up and I went for it just afterwards," he said.
"My (American) team mate Peter Stetina drove really hard and then it was up to me.
"I can accelerate really hard at the moment, afterwards there was a straight, long section which I knew would crack some of the other guys who were chasing, then I rode hard until the finish."
Second in the Tour of Catalunya last year, and third in the recent Brixia Tour in Italy, Martin says he will try to defend the yellow leader's jersey on Friday's 228-km ride through the Tatra mountains, the highest in Poland.
"It's a much longer stage, but the climbs are shorter so we'll have to see how it goes," he said. "We'd love to win this race ... but whatever happens just spending one day in the yellow jersey is a big honour."
The Tour of Poland ends on Saturday in Krakow.