Objective To more intuitively understand the quality control for laboratory animals and further achieving a more scientific and reasonable management of laboratory animals, the infection index as evaluation criteria was introduced. Then the best way to calculate infection index was explored in order to more scientifically reflect the infection status of laboratory animals. Methods Infection index, also called the degree of infection, is a qualitative indicator of monitoring laboratory animal quality. After arranging, analyzing, processing and gathering the data from laboratory animal quality monitoring, the index reflects synthetically the pathogen infection status or trend of a particularly investigated experimental animal population or the development of certain experimental animals. Results In general, the pathogen infection index of mice was slightly decreased, while the pathogen infection index of rats roughly increased year by year. In comparing infection index by different pathogens, the parasite infection index of mice was found to be higher than bacteria and virus infection indexes, while the bacteria infection index of rats was higher than parasite infection index and virus ones. Conclusions The infection index model intuitively reflects the quality control status of laboratory animals. The analysis also reveals that the parasite monitoring of the mice and the bacteria detection of rat needs to be reinforcement. In addition, the index of infection reveals that the pathogen infection of mice is well under control, while that of rats tends to be more serious year by year.