In this paper, data of 350 peasant households in five cities and counties of Jiutai, Dehui, Gongzhuling, Lishu and Qianguo, which locate in the corn belt area of Songliao plain, were selected for research data. Binary Logistic model was used to calculate the relevant factors of ecological compensation behavior of corn belt farmers in Jilin province. The research showed that the employment status of farmers, the disposal methods of pesticide and fertilizer wastes and the training of agricultural technology have a significant impact on the ecological compensation by farmers at the 1% level. A single farmer is willing to pay more time, capital and even technology in exchange for good market, high yield and more subsidies, so it has a high degree of correlation with compensation behavior. The original intention of the farmers is monetary compensation, and the sale of pesticide and fertilizer waste happens to realize the compensation behavior. Farmers who have trained in agricultural techniques are easier to implement compensation behavior. It is suggested that the government strengthen the subsidy to farmers and increase the enthusiasm to participate in ecological compensation, establish a long-term supervision and punishment mechanism for pesticide and fertilizer waste disposal, strengthen the guidance of farmers’ cognition, and appropriately popularize training in agricultural techniques.