This paper studies how does the individual enterprise of the middle and large-sized enterprises clusters choose its own innovation strategy between independent innovation strategy and imitative innovation strategy and what effect does its choice have on itself and the whole society through evolutionary game theory. The conclusions reveal that on one hand, the government's most basic policy on encouraging enterprises to innovate is the sound system of intellectual property rights protection; on the other hand, the government may adjust the ratio of the enterprises which make independent innovation to the enterprises which make imitative innovation in the middle and large-sized enterprises clusters by tax policy, cost subsidies and so on, so as to make this innovation ratio more reasonable and more stable.