Functional rice has been paid more and more attention because of the functions of adjusting human body's physiological function, improving human health and other characteristics. This study was conducted to analysis the genetic variation, correlation and principal component of 6 functional nutrition qualities of 226 japonica rice varieties in the cold region. Results showed that there are not significant difference in each functional nutrition qualities in two years,lysine, gluten, γ-Aminobutyric Acid（GABA）, flavonoids and average embryo weight, embryo of brown rice all have large variation of the 226 japonica rice varieties in the cold region. Among them, average embryo weight have the biggest variable coefficient, is 92.17%, flavonoids have the smallest variable coefficient, is 11.51%. Screen out of seven varieties(Suijing 3,Sujing 5,Mudanjing 21,Hejing 1,Mudanjiang 22,Longnuo 2,Xixuan 1) which have two higher functional nutrition components. Lysine content and average embryo weight, embryo of brown rice were all have extremely significant positive correlation; flavonoids content was significant negative correlative with GABA and significant positive correlative with gluten. The cumulative contribution of the embryo factor, flavonoids and gluten factor, GABA factor was 69.2%. In the process of functional variety breeding, should first pay attention to select big embryo, high GABA and low gluten and use marker-assisted selection or transgenic breeding means to realize polymerization breeding of multiple functional nutrition quality traits.