Objective To explore the value of whole process cleaning quality control in hospital disinfection supply center for risk prevention of hospital infection．Methods From January 2019 to June 2021,1000 surgical instruments to be cleaned and disinfected in the hospital disinfection supply center（observation group）were selected,and the whole process quality control was applied;another 1000 surgical instruments（control group）were selected for routine cleaning．The quality of instrument cleaning in the two groups was compared,and the hospital infection rate after the application of cleaned instrument was calculated．Results After cleaning and disinfecting instruments,the total incidence of blood stains,dirt and rust was 0.20% in the observation group,lower than that in the control group,which was 1.50%,and the qualified rate of instrument cleaning,disinfecting and sterilizing was higher than that in the control group（P<0.05）．The equipment operation procedures and standards,department management,safety management,and comprehensive quality management of the observation group were higher than those of the control group,the hospital infection rate was 0.10%,lower than that of the control group（1.00%）,and the satisfaction rate of medical staff was 95.00% in the observation group,higher than that of the control group（75.00%,P<0.05）．Conclusions The cleaning quality control of hospital disinfection supply center can improve the cleaning quality of surgical instruments and reduce the occurrence of hospital infection.