The white-belly and white-core mutants (WBRK and WCRK) from Wuyujing 3 were used to clarify the effects of nitrogen application levels (zero nitrogen application,CK; the ratio of basal N fertilizer to topdressing N fertrlizer for panicle initiation 1:1,N5-5; N fertilizer as basal fertilizer N10-0) on the occurrence of white-belly and white-core grains as well as grain chemical components. The results showed that Nitrogen application significantly increased the percentages of white-belly and white-core grains and the latter was more susceptible to nitrogen application. Averaged across nitrogen treatments, WBRK produced grains with similar chemical composition in comparison with those of control. By contrast, WCRK had higher total starch, amylose and amylopectin contents. Also, nitrogen application improved rice milling quality. Compared to CK, rice grains from WBRK showed significantly elevated contents of storage proteins except for albumin as nitrogen topdressing rate increased, while rice grains from WCRK contained significantly higher levels of protein with no significant changes in protein compositions. Nitrogen topdressing increased the contents of the majority of the 17 amino acids, but decreased histidine and arginine contents especially for WCRK. These findings suggested that nitrogen application exerted a significantly different influence on the occurrence of white-belly and white-core kernels and the accumulation of starch and protein during grain filling, indicating the necessity of various formulated strategies to eliminate white-belly and white-core grains.