To compare comprehensively the benefits of radiofrequency ablation (RFA) and percutaneous ethanol injection (PEI) with those of surgical resection (SR) in early-stage hepatocellular carcinoma (HCC). The potentially relevant studies comparing the efficacy and safety of RFA and/or PEI with those of SR were searched using the databases such as PubMed, MEDLINE, Embase and Chinese databases (CNKI and Wanfang data). Overall survival rate, recurrence-free survival rate and complications were compared and analyzed. Pooled odds ratios with 95 % confidence intervals (95 % CIs) were calculated using either the fixed-effects model or random-effects model. All statistic analyses were conducted using the Review Manager (version 5.1.) from the Cochrane Collaboration. Our analysis showed that the overall survival rate in patients treated with SR was significantly higher than that of percutaneous ablation therapy (PAT) [SR vs. PAT: 95 % confidence interval (95 % CI)2-year 0.46–0.89, P = 0.009; 95 % CI3-year 0.57–0.83, P