The article selects 13 financial indicators of listed companies to build the M&A performance of pharmaceutical industry evaluation system, and analyzes38 Chinese listed companies in the pharmaceutical industry, uses factor analysis analyze financial data samples from 2007 to 2012,extracts four common factors, establishes evaluation model of M&A performance, gets a composite score of M&A performance, and compares the M&A performance score results, then, judging from the result of the six years of M&A performance to show that the trend towards rising. According to the results of the factor analysis, we propose some politic recommendations based on the microscopic aspects for the M&A in pharmaceutical industry and hope to promote the development of the pharmaceutical companies healthily and orderly.