This meta-analysis aims to compare corneal injuries and function after femtosecond laser-assisted cataract surgery (FLACS) and conventional phacoemulsification surgery (CPS). A comprehensive literature search of PubMed, EMBASE, and the Cochrane Controlled Trials Register was conducted to identify randomized controlled trials (RCT) and high-quality prospective comparative cohort studies comparing FLACS with CPS. Endothelial cell loss percentage (ECL%), central corneal thickness (CCT), endothelial cell density (ECD), endothelial cell loss (ECL), percentage of the hexagonal cell (6A), and coefficient of variance (CoV) were used as an indicator of corneal injury and function. Totally 42 trials (23 RCTs and 19 prospective cohort studies), including 3916 eyes, underwent FLACS, and a total of 3736 eyes underwent CPS. ECL% is significantly lower in the FLACS group at 1-3 days (P = 0.005), 1 week (P = 0.004), 1 month (P<0.0001), 3 months (P = 0.001), and 6 months (P = 0.004) after surgery compared to CPS. ECD and ECL appeared no statistically significant difference between the two groups, except for the significant reduction of ECD at 3 months in the CPS group (P = 0.002). CCT was significantly lower in the FLACS group at 1 week (P = 0.05) and 1 month (P = 0.002) early postoperatively. While at 1-3 days (P = 0.50), 3 months (P = 0.18), and 6 months (P = 0.11), there was no difference between the FLACS group and the CPS group. No significant difference was found in the percentage of hexagonal cells and the coefficient of variance. FLACS, compared with CPS, reduces corneal injury in the early postoperative period. Corneal edema recovered faster in the FLACS group in the early postoperative period. In addition, FLACS may be a better option for patients with corneal dysfunction.