In order to explore the regulation mechanism of genome-wide DNA methylation at rice seedlings upon low temperature stress treatment， three rice genotypes showing levels of cold tolerance were treated at 3-4 ℃， followed by determination of the genome-wide DNA methylation using whole genome bisulfite sequencing （WGBS）. By analyzing the distribution of methylation-related genes in the promoter and genic body region of the three samples， it was found that the related genes were mainly distributed in the promoter region. The genotype P427 was found anchoring the highest number of genes， including 9223 genes in the promoter region， and 2906 genes in the body region. The genotype 9311 was found anchoring the fewest genes. GO and KEGG enrichment analysis revealed that the differentially methylated genes were mainly involved in metabolic pathways such as those of diterpene biosynthesis， starch and sucrose metabolism， β-alanine metabolism， and phenylpropane biosynthesis. These results indicated that the methylation in the promoters was important in the regulation of low temperature stress-responsive genes， and the transcriptional regulation was associated with the degree of methylation and the methylation types. The genotype P427 may affect the cold tolerance of rice through modulating the genes in metabolic pathways such as diterpene biosynthesis， starch and sucrose metabolism， and hormone signal transduction pathways. Collectively， these results provided better understanding of the methylation-based response mechanism of cold tolerance in rice