For investigation of DNA methylation level in Huainan pigs at different developmental stages, and screening differential methylation level of muscle regulating genes, we performed the whole genome methylation sequencing and selecting the candidate genes by analysis of pathway with longissimus dorsi muscle of Huainan boars at days 38, 58, 78 days post coitus (dpc) and 21 postnatal days. The results showed that methylation level of mCpG in gene body regions was higher than that of in upstream 2K and downstream 2K gene regions, and its highest methylation level in elements were intron, 3’UTR and repeat sequence. During the development, the methylation level in gene body regions was decreased, and it in upstream 2K and downstream 2K of gene regions was with a trend of down-up-down. The methylation level of intron, 3’UTR and repeat sequence were gradually decreased, while the methylation level of promoter regions had a trend of down-up-down. Pathway enrichment analyses were carried out, and the results showed that CpG methylation of focal adhesion (P=0.0009，P=0.0004, P=0.0001) and CHH methylation of adherents junction (P=0.0132, P=0.0128, P=0.0005) were both highly significant difference in the adjacent development stage of Huainan pigs. By bioinformatics analyses, ACTN4 and FGFR1 as candidate muscle development genes were screened out from these pathways. In conclusion, the differential methylation genes of longissimus dorsi muscle were found during different developmental stages in Huainan pig breed, and two genes which effecting the capacity of binding to actin and the differentiation of muscle cell were selected as candidate genes effecting muscle development. The changes of methylation levels of two genes will contribute to understand the molecular mechanisms of muscle development.