Objective To explore the application effect of comprehensive quality control management in disinfection of oral implant instruments. Methods From April 2022 to May 2023, 250 oral implant instruments in the Department of Stomatology of our hospital were selected as the research objects. According to the different quality control management methods, they were divided into control group and observation group, with 125 instruments in each group. The control group was given routine management, and the observation group was given comprehensive quality control management. The disinfection, infection control and disinfection quality of the two groups were compared. Results The qualified rate of sterilization and packaging in the observation group were higher than those in the control group, and the equipment loss rate and infection rate were lower than those in the control group, the differences were statistically significant (P<0.05). The scores of process specification, cleaning work, disinfection work and equipment management in the observation group were higher than those in the control group, and the differences were statistically significant (P<0.05). Conclusion The application of comprehensive quality control management in the disinfection of oral implant instruments is effective, which can effectively improve the qualified rate of sterilization and packaging, reduce the loss rate of instruments, help to improve the quality of disinfection, and achieve good infection control effect.