Precision hepatectomy for primary liver cancer has been widely used in clinical practice. As an effective nutritional supplement to prevent endotoxemia and hepatic impairment, microecological agents have been used together with traditional enteral nutritional support substances in several clinical studies. Chinese and English databases were searched using the terms "hepatocellular carcinoma", "hepatectomy", "microecological agents", and "microecological regulators". The search terms were "hepatocellular carcinoma", "liver resection", "microecological agents", and "microecological regulators". Meta-analysis was performed using Rev Man 5.3 and Stata 13 software provided by the Cochrane system. Eleven randomized controlled trials (RCTs) were included in this study. Of these, all 11 described the correct method of random assignment; 8 described in detail the concealment of the assignment scheme; and 9 used blinding methods in the research. Microecological agents significantly reduced total bilirubin (TBIL) levels [mean difference (MD)=-0.10, 95% confidence interval (CI): (-0.14, -0.06), P<0.00001] of patients after hepatectomy. The alanine transaminase (ALT) levels [MD =-3.65, 95% CI: (-14.65, 7.34), P=0.52], aspartate aminotransferase (AST) levels [MD =-0.64, 95% CI: (-6.87, 5.58), P=0.84], prothrombin level [MD=1, 95% CI: (-2.57, 4.57), P=0.58], and C-reactive protein (CRP) level [MD =-0.28, 95% CI: (-3.01, 2.45), P=0.84] among the included articles were statistically significant. However, probiotics could significantly reduce the risk of postoperative infection in patients with liver cancer (MD =0.23, 95% CI: (0.07, 0.79), P=0.02 <0.05), and did not significantly increase the risk of complications in patients with liver cancer [odds ratio (OR) =0.82, 95% CI: (0.38, 1.77), P=0.61]. This study used meta-analysis to confirm that microecological agents can significantly improve the immune function of patients with hepatocellular carcinoma, and have alleviating effects on endotoxemia and hyperbilirubinemia.