In order to explore the significance of healthiness degree of plan and evaluation mechanism and verify the feasibility of the quantitative methods， this study collected all of the relevant documents of infectious disease prevention and control published in Zhejiang and Shanghai from 2000 to 2017. From the documents， we extracted and quantified the relevant fields， and comprehensively formed the quantitative index “healthiness degree of plan and evaluation mechanism”， compared the time series changes and similarities of healthiness degree of plan and assessment mechanism of infectious disease system between Zhejiang and Shanghai， and analyzed the relationship between the incidence of Class A and B infectious disease. The results showed that the healthiness degree of plan and evaluation mechanism of infectious disease system between Zhejiang and Shanghai had improved gradually from 2000 to 2017. The trend of incidence of notifiable infectious diseases showed significant negative correlation to that of the coverage in these two places （P<0.01）. By the end of 2017， the plan and evaluation mechanism for infectious diseases in Zhejiang and Shanghai has been initially improved. However， the two places still had problems of low coverage of evaluation indicators and weak implementation. By proposing corresponding policy recommendations， it is expected to further improve the plan and evaluation mechanism.