Objective To comprehensive evaluate the disinfect effect of glutaraldehyde, ortho-phthalaldehyde (OPA) and peracetic acid on gastroscopy disinfection. Methods Retrieval all the relevant literature from PubMed, Cochrane Library, web of science, Embase, CNKI,CBM, VIP to collect the randomized controlled trials about glutaraldehyde, OPA and peracetic acid disinfection on gastroscopy. According to the inclusion and exclusion criteria to select the literature, extract data and make a Meta-analysis used the RevMan5.3.4.0 statistic software. Results 18 RCT trials were included. The disinfection of OPA group and glutaraldehyde group had statistical significance (OR=2.02,95% of the CI were (1.88, 1.27), P<0.00001). The disinfection of peracetic acid group and glutaraldehyde group had statistical significance (OR=2.79, 95% of the CI were (1.52, 5.11), P=0.0009). The disinfection of OPA group and peracetic acid group had no statistical significant (OR=1.30, 95% of the CI were (0.67, 2.3), P=0.49). Conclusions The disinfection effects of OPA and peracetic acid on gastroscopy are better than that of glutaraldehyde, and there is no statistical difference between OPA and peracetic acid. However, peracetic acid is low cost and no corrosiveness comparing with OPA. Therefore, the better choice of disinfectant on gastroscopy is peracetic acid.