Truex, driving the No.1 Earnhardt-Ganassi Chevrolet, grabbed the pole position with a best-lap speed of 188.001 mph (47.872 seconds).
"It's a big deal starting on the pole for the Daytona 500," Truex said after capturing the prime spot for the second time in his Sprint Cup career.
Truex won the NASCAR Nationwide Series championship in the 2004 and '05 seasons.
Martin, driving the No.5 Hendrick Motorsports Chevrolet for the first time, earned the No. 2 position (the outside pole) with a second-best time of 47.919 seconds.
Ryan Newman, the 2008 race winner, finished third in qualifying, followed by Juan Pablo Montoya and Bill Elliott.
Two-time points champion Jimmie Johnson, Aric Almirola, Travis Kvapil, Jeff Gordon and Tony Stewart grabbed the remaining spots in the top 10.
The final positions in 43-driver field will be determined Thursday.