Objective To systematically review the efficacy of chlorhexidine versus povidone iodine in the prevention of wound infections after surgeries by meta-analysis. Methods All randomized controlled trials comparing these two disinfectants were searched from databases of PubMed, The Cochrane Library (Issue 3, 2016), EMbase, WanFang Data, VIP and CNKI from inception to August 2016. Two reviewers independently screened literature, extracted data and assessed the risk of bias of included studies. Then, meta-analysis was performed using RevMan 5.2 software. Results A total of 14 randomized controlled trials were included. The results of meta-analysis showed that the chlorhexidine group had significantly lower rates in any surgical site infection (RR=0.71, 95% CI 0.58 to 0.88,P=0.001) and superficial incisional infection (RR=0.66, 95% CI 0.48 to 0.91,P=0.01) when compared with povidone iodine group. However, there were no significant differences in deep incisional infection (RR=0.51, 95% CI 0.23 to 1.11,P=0.09) and organ-space infection (RR=0.97, 95% CI 0.53 to 1.76,P=0.92) between the two groups. Furthermore, subgroup analysis revealed differences in any surgical site infection and superficial incisional infection could only be found in surgeries possibly contaminated. Conclusion Chlorhexidine may be superior in decreasing the incidence of infection in probably contaminated surgery.