【Abstract】 Objectives To explore scientific packaging time and focus on the correlation between storage time as well as environment and the pollution degree of surgical instruments after cleaning in different ways. Methods 960 contaminated surgical instruments were divided into group A，group B，group C and group D. The surgical instruments from group A and group C were cleaned by manual cleaning. While the surgical instruments from group B and group D were cleaned by machine cleaning. At the same time, all the instruments from group A and B were stored in clean environment. As a comparison, the ones from group C and D were stored in common environment. All the surgical instruments were sampled with ATP bioluminescence tester at 6 time points after cleaning. The risk factors of the pollution degree and relationship were analyzed.Results Machine cleaning was better for manual cleaning (P＜005). The risk factors of instrumentcontaminated including time, environment and cleaning methods (P＜005). It had conformance tendency between the percent of pass, cleaning methods, environment and time（2=6603，P=000）. Conclusion In clinical work, the surgical instruments after cleaning should be packed in time. The surgical instruments stored in common environment are supposed to be packed in 2 hours, and which stored in clean environment should be packed in 6 hours to ensure the high quality of cleaning.