Innovation organization has a significant impact on innovation performance，because product innovation and process innovation have a difference factor intensities degree of knowledge, technology and skills. Taking 7499 R&D manufacturing enterprises as the reference group, we estimate the innovation performance and its influencing factors of 4833 strategic emerging industrial product and process innovation in Jiangsu province by using the dual logarithm regression model. The Government R & D subsidies have a significant direct impact on the product and process innovation of the reference group, and no significant effect on the target group. Further study found that the individual enterprises subsidies strength of the target group is lower, not to cross the lowest "R&D Investment Threshold". The effect of Industry-University-Research cooperation on product innovation of the target group was greater than that of the reference group, and the effect of the process innovation was less than that of the reference group. The cross terms of government R&D subsidies and Industry-University-Research cooperation has significant effect on the product innovation of the target group, which has no significant effect on the process innovation. Based on the empirical conclusion, the paper puts forward some policy suggestions on the strategic emerging industrial product and process innovation efficiency from the perspective of R&D subsidies and the mode of cooperation.