To better identify people at high risk of developing hepatocellular carcinoma (HCC) in non-alcoholic fatty liver disease (NAFLD), we aimed to conduct a systematic review and meta-analysis. Databases (including MEDLINE, EMBASE, Web of Science, the Cochrane Library, ClinicalTrials.gov) were searched up to March 2021. We included studies that reported odds ratios (ORs) or hazard ratios (HRs) and 95% confidence intervals. 24 studies (3 prospective cohort studies, 16 retrospective cohort studies, and 5 case-control studies) of 23 articles, with a total of 1004284 NAFLD cases and 3610 NAFLD-HCC cases, were finally included. The pooled data suggested male, older age, diabetes, low platelet count, and advanced liver fibrosis were important risk factors for HCC in NAFLD. Hypertension, overweight, low albumin, PNPLA3 genotype, dyslipidemia, abnormal liver enzymes were also risk factors worth concern. This study may contribute to the establishment of targeted screening and secondary prevention of HCC in patients with NAFLD.