The aim of this study was to meta-analyze the association between apolipoprotein C3 gene (APOC3) polymorphism and the susceptibility of non-alcoholic fatty liver disease (NAFLD). Several databases, including PubMed, Embase, SpringerLink, Wanfang and Chinese National Knowledge Infrastructure (CNKI) were searched for relevant studies published before February 1, 2016. Hardy-Weinberg equilibrium (HWE) test was performed by using Stata11.0. The odds ratio (OR) and the 95% confidence interval (CI) were used as the effect sizes (ESs) to assess the association. Revman 5.2 software was used to pool the ESs. This meta-analysis included nine studies published during 2010-2014. There were 3977 subjects containing 2111 cases and 1866 controls. The results for both APOC3 C482T and T455C under all models (P>0.05) or the combined model (OR=1.00, 95% CI: 0.84-1.19, P=0.98) were not significant. These results indicate that there is no association between APOC3 polymorphisms (C482T and T455C) and NAFLD susceptibility.