The Ko-Osnac02 mutant matured earlier than the wild type (WT) in 15 days obviously. The result showed that the Ko-Osnac02 chalky with white-core and white-belly mature endosperm. The seed filling rate plays a major role in determining the yield and quality of rice (Oryza sativa L. versus japonica). Interestingly, in the Ko-Osnac02 seeds, higher amylose content (AC) was observed in vegetative endosperm (5DAP), while lower amylose content (AC) and higher soluble sugar content were observed in the mature endosperm. RNA-Seq analysis of N2/N3 seed (3DAPs) and the WT revealed that among the top differentially expressed genes (DEGs), the OsBAM2 (LOC_Os10g32810) expressed significantly high which involved in starch degradation. In addition, seven genes were expressed at a lower-level in pro-pro interactions inducing the chalky endosperm formation in N2 mutant seeds (3 DAP), which could be verified by heatmap diagrams based on DEGs of N2 versus WT. The cell cycler controlling the Tubulin genes downregulated their expression together with the MCM family genes MCM4 ( ↓ ), MCM7 ( ↑ ), which may cause white-core in the early endosperm development. In conclusion, the developing period shorten significantly in the Ko-Osnac02 mutants may cause the chalkiness in seeds during the early endosperm development.