Fertilizer input structure affects the rational utilization and allocation of resources,and it also has the influence on the sustainable development of agriculture.Based on the on- the- spot survey data from 620 growers in 7 apple producing provinces,this paper analyzes the farmer’s fertilizer input structure and its influencing factors with the help of simultaneous equation model.The result shows that there is a complementary relationship between the two fertilizers’ input.Disasters and signing sale contracts have the postive imapct on chemical fertilizer input and negative impact on organic fertilizer input significantly.The proportion of non- agriculture income,planting density and the convenience of irrigation have the negative impact on fertilizer input,and the positive influence on organic fertilizer input.The price and settlement of chemical fertilizer have a positive impact on chemical fertilizer input,and raising livestock will decrease the organic fertilizer input significantly.Therefore,this paper proposes several suggestions,such as establishing the awareness of correct fertilizer management,making sure that farmers have adequate organic chemical fertilizer,increasing the utilization efficiency of fertilizer and overcoming the funds restriction of farmer’s fertilizing.