Genetic and difference of total flavonoids and alkaloids content are studied, based on germinated brown rice and brown rice of 222 RILs as well as their parents. The results show that total flavonoids and alkaloids present a wide range of genetic variation in germinated brown rice and brown rice of RILs, the total flavonoids content in brown rice is slightly higher than germinated brown rice, but all appear the normal distribution and similar to the qualitative traits the distribution. Total alkaloids content in germinated brown rice is 1.5 times as much as the brown rice, but all appear the skewed distribution. This study can be a theoretical basis for genetic and breeding of the functional rice..