Based on the Brand Architecture Strategy Theory, this paper puts forward the concept of brand architecture fitness and proposes the research hypotheses through theoretically analyzing how different brand architecture combinations between the acquiring party and the acquired party of M&A affecting the long-term performance of the acquirer. The empirical test uses the data of Chinese A-share listed companies which complete 100%equity M&A from 2010 to 2016, and establishes a control group based on the A-share listed companies that do not participate in M&A at the same time. With the panel data and multiple empirical analysis method, the results show that the long-term performance of the acquirer is higher when the brand architectures of both sides are inconsistent than that of both are consistent. More specifically, under the consistent situations, the long- term performance with house of brands architecture of both sides of M&A is higher than that with branded house architecture of both sides; while under the inconsistent conditions, no matter what brand architectures the both sides of M&A are, there are no significant differences in the long-term performances after M&A. In addition, there exist heterogeneous effects due to the factors such as brand equity gap between the two sides of M&A. This study extends the research on the brand effects of M&A from the impact of brand architecture characteristics of both sides on the short-term performance of M&A to the influence of the brand architecture fitness of both sides on the long-term performance, which provides valuable guidances for enterprises to better select the M&A target companies and gain higher long-term performances after M&A.