Indigenous rice has maintained the survival of local people for more than a thousand years in the Yuanyang terraced rice fields of southern Yunnan, China. It is the foundation for long-term stable development of local agriculture and food security and its unique and irreplaceable characteristics give the terraces value. The status of indigenous rice resources is threatened by serious loss, so a better understanding of rice diversity and the factors that influence rice variety protection is conducive to policy. Here, we investigate the planting and conservation situation of indigenous rice, analyze factors impacting the protection and loss of traditional rice varieties, and construct an indigenous rice protection influence index system. Controllable factors which have special meaning to the maintenance and management of local rice are identified and corresponding strategies for the protection and maintenance of indigenous rice are discussed.