For innovative enterprises, sustainable innovation is the key to obtain and maintain competitive advantage. However, after ten years of construction and evelopment of innovative enterprises in China, some enterprises have shown the situation that they can weaken the ability of sustainable innovation, and even can not maintain innovation. According to the existing foundation of innovation and the need for their sustainable development of innovative enterprises, this paper expounds the significance of the merger and acquisition (M & A) as an important way to realize the sustainable innovation. At the same time, a method of M & A decision is proposed, which takes into account the return to scale (RTS) of undesirable output. Firstly, a Generalized Data Envelopment Analysis (GDEA) model and a WY-DEA model with undesirable output are established, which are based on the judgment method of scale income which is limited to the desirable output. Secondly, the Generalized DEA model is used to determine whether the RTS of the weak WY-DEA effective M{\&}A schemes are constant, increasing, decreasing or crowded. Then on the basis of the elimination of the congestion plan, the cross efficiency model is used to select the optimal purchasing party. Finally, a numerical example is given to illustrate the feasibility and advantage of the method.
