This paper analyzes the degree of prevention and control of the allocation of financial resources in Zhejiang and Shanghai, the degree of prevention and control in the field of infectious diseases, and its correlation with the incidence of Class A and Class B infectious diseases. The test evaluates the prevention and control of infectious diseases based on appropriate financial resources allocation. effect. Use China Knowledge Network (CNKI) to collect research literature on the financial input of the government in different years in Zhejiang and Shanghai, the appropriateness of the total amount of financial input, and the steady growth of fiscal investment, systematically collecting all infectious diseases involving Zhejiang and Shanghai. The literature on prevention and control work comprehensively quantifies the degree of support for the allocation of financial resources. Spearman correlation and linear regression were used to analyze the relationship between the appropriateness of financial resources allocation and the incidence of infectious diseases. Through the results, it was found that the appropriateness 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 appropriateness of financial resources allocation in the two places (p<0.01). Therefore, the financial resource allocation appropriateness system should establish an input and compensation mechanism with appropriate investment, strong support and stable growth; the appropriateness of the allocation of financial resources in Zhejiang and Shanghai is generally rising, but the government is not clear in financial input, and the financial input lacks quantitative standards. It is difficult to assess, and the growth mechanism is imperfect and the financial growth is unstable. The allocation of financial resources in the two places has contributed to reducing the incidence of infectious diseases, and the performance of Shanghai is more obvious; the method of quantifying the appropriateness of financial resources allocation is feasible.