This paper analyzes the appropriate degree of prevention and control of the allocation of financial resources in Zhejiang and Shanghai. It was found in the results that the appropriate degree of the allocation of financial resources in Zhejiang and Shanghai increased year by year from 2001 to 2017. By 2017， the proportion of financial resources allocation in Zhejiang and Shanghai will account for 45.3% and 62.0% respectively. There was a significant negative correlation between the incidence of infectious diseases of Class A and B and the appropriate degree of financial resources allocation in the two places. Therefore， appropriate degree of the financial resource allocation system should establish an input and compensation mechanism with appropriate investment. The allocation of financial resources in the two places had contributed to reducing the incidence of infectious diseases， and the performance of Shanghai was more obvious； the method of quantifying the appropriateness of financial resources allocation was feasible.