Polydatin (PD), a natural precursor of resveratrol, has been used to treat several diseases, such as cardiovascular diseases, hepatic diseases and various cancers. In this study, we aimed to investigate the protective effects and underlying mechanisms of PD on non-alcoholic fatty liver disease (NAFLD) using a high fat induced obese mice model. The studied subjects were randomly divided into a lean group, a high fat diet (HFD) group, and a high fat diet with PD (HFD + PD) group. The results showed that PD reduced the body weights in HFD mice. PD also downregulated the serum levels of triglyceride (TG), low density lipoprotein (LDL), aspartate aminotransferase (AST) and alanine aminotransferase (ALT), and upregulated high density lipoprotein (HDL). Moreover, PD significantly alleviated hepatocyte steatosis and reduced Gr-1 cells in the liver tissues of HFD mice. The mRNA levels of pro-inflammatory factors, such as monocyte chemoattractant protein-1 (MCP-1), tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), S100A8 and S100A9 were significantly decreased in the liver tissues of HFD mice with PD treatment, and the downregulation of MCP-1 and S100A9 protein expressions was also observed. In conclusion, PD had beneficial roles in suppressing lipid accumulation in hepatocytes and anti-inflammatory responses in the liver tissue of obese associated NAFLD.