DNA methylation is an important epigenetic marker in eukaryotes, and could affect chromatin structure and gene expression. With the development of genome-wide methylation sequencing technology, DNA methylation level in the whole genome can be evaluated. In this review, we summarize the research progress of DNA methylation on promoter, gene body, enhancer, silencer and transposon, as well as the relationship between DNA methylation and gene expression. DNA methylation of gene promoter suppresses gene expression, while the relationship between DNA methylation of gene body and gene expression depends on species and cell types. The gene activity is inversely related with the DNA methylation level of enhancer, but positively correlated to the DNA methylation of silencer. Transposon hypermethylation restricts its transposition activity to maintain the genome stability. Furthermore, we discuss the interaction between DNA methylation and histone methylation, its roles in regulation of gene expression, alternative splicing and transcription, and directions for future studies in this field.