Abstract: The collaborative innovation among government, institute and enterprises is an advanced form of industry-university-research collaborative innovation and a new paradigm of scientific and technological innovation in modern times. From the perspective of symbiotic theory, on the basis of expounding the correspondence between the symbiotic theory and the collaborative innovation of government, institute and enterprises, the analysis on the symbiotic system of collaborative innovation among the government, institute and enterprises was carried out, and the restrictive factors of collaborative innovation among the government, institute and enterprises were analyzed. Furthermore, the optimization strategies were put forward for the collaborative innovation among the government, institute and enterprises, in order to promote the establishment of a long-term mechanism for the multi-party participation, efficient coordination and benefit sharing among the government departments, agricultural scientific research institutes and enterprises.