Diesel exhaust (DE) can enter the organism body and cause multiple organ damage. DE contains particles that can be suspended in the air for a long time. Epigenetic regulation is a post transcriptional regulation change that does not involve DNA sequence changes. Many evidences showed that DE can affect the normal physiological functions of multiple organs and systems through epigenetic changes, thus regulating the occurrence and development of multiple diseases. This paper reviewed the research progress of DNA methylation and non-coding RNA in the biological harmful effects of DE. This will provide a basis for the safety evaluation, health risk assessment, and management of DE.