Indigenous rice, which can grow at higher altitudes, contains unique genes and genetic characteristics, but its future survival is uncertain. The conservation of indigenous rice is of great significance from the perspectives of both germplasm resource conservation and economic value. This paper puts forward suggestions for indigenous rice conservation in Yuanjiang County based on the stakeholder theory and the results of the three-party evolutionary game model involving the local government, enterprises or cooperatives, and farmers. This paper also provides references for the conservation and sustainable utilization of agricultural biodiversity and genetic resources in other crops. The results of the three-party evolutionary game model showed that in the short term, the protection of indigenous rice is in urgent need of encouragement and guidance from governments. This study found a close relationship between subsidies from the government and enthusiasm for buying and planting indigenous rice among enterprises as well as farmers. When the coefficient of governmental subsidy was low, enterprises tended to “not purchase”. On the contrary, when the coefficient of governmental subsidy was higher, the enterprises reached an evolutionary stable state faster, but the government reached the evolutionary stable state more slowly. When the coefficient of governmental subsidy to farmers was large, farmers tended to “do not plant” and the government tended to “do not encourage”. Therefore, the government should carefully weigh the subsidies, and take into account the local financial situation and the status quo of the restoration of indigenous rice planting as well as in-situ protection.