Employing firm level data of Chinese family enterprises Panel Data over the period of 2009-2012, this paper empirically tests the relationship between the degree of the ownership and the innovation performance, the moderate effect of government-enterprises, the number and the structure of independent directors and regional marketization. Finding that there is inverted u-shaped relationship between the degree of ownership and innovation performance. The number and the structure of independent directors play a negative moderating role on the relationship between the degree of ownership and R&D. Government-enterprise relationship plays a not significant moderate effect on the relationship between R&D and innovation performance, while Regional marketization plays a positive moderate effect. High regional marketization plays a significantly negative moderating role while the Government-enterprise relationship makes a significantly positive moderating role.Through the above results, this paper gives a new perspective to explain the relationship between the ownership and innovation performance in family enterprises.