Seed dormancy and germination are critical agricultural traits influencing rice grain yield. Although there are some genes have previously identified, the comprehensive understanding on large-scale transcriptome is deficient. In this study, we generated mutants of two representative regulators of seed germination, Oryza sativa Viviparous1 (OsVP1) and Seed dormancy 4 (Sdr4), by CRISPR/Cas9 approach and named them cr-osvp1 and cr-sdr4. The weakened dormancy of mutants indicated that the functions of OsVP1 and Sdr4 are required for normal early seed dormancy. In the transcriptome sequencing analysis, 4157 and 8285 DEGs were identified in cr-osvp1 vs. NIP and cr-sdr4 vs. NIP groups, respectively, with a large number of overlapped DEGs that have similar expression patterns in two groups.The GO and KEGG enrichments showed that genes related to carbohydrate metabolic, nucleoside metabolic, amylase activity and plant hormone signal transduction were involved in the dormancy regulation. These results indicated that OsVP1 and Sdr4 play an important role in regulating seed dormancy that involved in multiple metabolism and regulatory pathways. The systematic analysis of the transcriptional level changes provides theoretical basis for the research of seed dormancy and germination in rice.