Innovation alliance is an important platform for integrating complementary resources and carrying out collaborative research. In order to promote the sustainable and healthy development of the alliance, the key for the government is to grasp the potential impact of various incentive measures on the collaborative behavior of alliance members. In view of this, the classified construction and management practices of National Agricultural Science and Technology Innovation Alliance were considered. And the three tripartite evolutionary game models including research institutes, upstream enterprises and downstream enterprises, were constructed. Specifically, the heterogeneous impact of potential interventions, such as government subsidies beforehand(GSB), government cost subsidies afterward(GSA) and government rewards afterward(GRA), on the collaborative ecosystem within industrial, professional or regional alliances was considered. In the end, the incentive effects of governmental interventions were simulated. It turns out that additional funding initiatives by central government are necessary. Furthermore, GSA for all active collaborators is the key to promote active collaboration among alliance members. And professional alliances have a strong demand for it, followed by industrial alliances and regional alliances. In addition, the higher intensity of GSB for the dominant party can also motivate the members of industrial alliances to collaborate actively.