Abstract University mergers fundamentally aim to enhance the level of higher education and scientific research performance through resource integration by “reorganization”. However, whether university mergers achieve the latter goal has been subject to controversy. With the help of the “quasi-experiment” of Chinese colleges and universities merged in the 1990s, this study determines the impact of university mergers on scientific research performance. Panel data of 431 colleges and universities from 1993 to 2013 in The compilation of scientific and technical statistics of Chinese higher education and difference in differences method are used. Results show that the merger of colleges and universities exert a significant negative impact on the scientific research performance due to excessive government interventions and difficulties in cultural integration. The merger effect is related to the number of university participants and degree of government intervention. Therefore, university mergers cannot effectively promote the level of scientific research, unable to bring economies of scale and rather lead to diseconomies of scale.