Genetic and difference of GABA and RS are studied, based on germinated brown rice and brown rice of 222 RILs as well as their parents, to breed new varieties of high content of GABA and RS. The results show that The different of GABA content between germinated brown rice and brown rice of RILs is not significant. GABA content present a wide range of genetic variation in germinated brown rice and brown rice, controlled by major gene. RS content in germinated brown rice is 1.2 times as much as the brown rice. RS content present a wide range of genetic variation in germinated brown rice and brown rice, but all appear the skewed distribution. High altitude and cold climate were effective to improvement and evolution of high content of resistant starch of brown rice.This study can be a theoretical basis for genetic and breeding of the functional rice.