Through a study of M&A data of listed companies between 2011 and 2013, this paper discusses the influence of corporate capital structure on its performance after M&A from the perspective of internal control. It is found that leverage gap is negatively related to M&A performance and internal control has significant positive influence on this relationship. This positive influence from internal control is less significant in SOEs than in private enterprises, which is attributed to the fact that M&A in SOEs is not entirely the result of effective allocation of resources because of political interference. Meanwhile, the negative influence from leverage gap is more significant in SOEs than in private enterprises, which is attributed to the fact that capital operation efficiency in SOEs is lower than in private enterprises because of the soft constraint of government budget, more agent problems and overconfidence in management. The conclusion shows that from the perspective of microeconomic M&A, it is of practical significance to improve the level of internal control and the scientific allocation of capital structure.