With the increasing number of international joint ventures (IJVs), both sides of the joint venture want to gradually achieve their strategic objectives through IJVs, so they compete fiercely for control, which eventually leads to the decline of innovation performance. In order to explain and avoid this phenomenon, this paper took 225 IJV enterprises in the 2018 manufacturing enterprise innovation questionnaire as samples, and constructed a hierarchical regression model to empirically test the relationship between IJV''s control mechanism and innovation performance, as well as the regulatory effect of innovation capital source structure. The results show that: The balanced shareholding structure of the two parties can bring the highest product and process innovation performance to IJV, followed by The Chinese party is the second, and the foreign party is the lowest; There is an inverted U-shaped relationship between the IJV intellectual property protection and the product innovation performance, and there is a significant linear positive correlation between the number of process innovation performance; Cultural control has a significant positive impact on the innovation performance and process innovation performance of IJVs; The structure of innovation funding sources will significantly and positively adjust the relationship between intellectual property protection and process innovation performance, and the external-led innovation funding source structure has the highest positive adjustment effect, followed by internal dominance, and the lowest equilibrium type. At the same time, it also proposes countermeasures for IJV in China to seize control and improve innovation performance.