With the rapid development of the economy and society, people began to pay more attention to their own health, which has also boosted the rapid progress of the pharmaceutical industry. The pharmaceutical industry is an important industry related to people's livelihood. The financial performance evaluation of enterprises is of great significance for the development of the industry. This paper will use big data retrieval to select 25 pharmaceutical enterprises listed on the National Equities Exchange and Quotations(NEEQ).Relying on big data comprehensive research results, we have summarized the representative assessment indicators. At the same time, according to the product category, development history, financial situation, market prospects and other conditions, we cluster and analyze 25 enterprises in SPSS software, and obtain six representative pharmaceutical enterprises in China. Finally, we use the principal component analysis method and the fuzzy comprehensive appraisal method to rank the performance evaluation of these enterprises, to help enterprises to clearly understand their own position in the industry, and fully understand the situation of competitors in the industry, and explore new development directions.