A novel method was developed for the determination of trace lead and cadmium in transgenic brown rice based on separation and preconcentration with a micro column packed with crosslinked carboxymethyl konjac glucomannan (CCMKGM) prior to its determination by graphite furnace atomic absorption spectrometry. Variables affecting the separation and preconcentration of lead and cadmium, such as the acidity of the aqueous solution, sample flow rate and volume, and eluent concentration and volume, were optimized. Under optimized condition, detection limits of the method for the determination of trace lead and cadmium in transgenic brown rice were 0.11 and 0.002 μg·L-1, respectively. The obtained results of lead and cadmium in the certified reference material (GBW10010, GBS1—1) were in good agreement with the certified values. The recoveries were in the range of 90%～103% and 93%～105% for detection of Pb and Cd in transgenic brown rice and the wild-type brown rice samples respectively. This study could provide technical support for determination of trace Pb and Cd in transgenic rice.