Heilongjiang Province, as a major grain-planting province in China, under the condition of limited production level and cognitive level, the food and agriculture industry often adopts the “high input-high output” production model to achieve grain yield and increase production. As one of the important material input elements in agricultural production, chemical fertilizer plays an irreplaceable role in increasing crop output and farmers’ income. The reduced application of chemical fertilizer can improve the soil and water source, improve the production environment from the internal agricultural production, and ensure the quality and safety of agricultural products from the source, which is beneficial to the sustainable development of agriculture in China. In this paper, Probit model is used to analyze the risk preference and risk perception of grain farmers in Heilongjiang Province. The results showed that high degree of risk preference had a negative effect on decision behavior of fertilizer application, while high natural risk perception had a positive effect on fertilizer application behavior of grain farmers. At the same time, the results showed that the cultivated land area owned by farmers, the total income of agricultural production, the training of fertilizer technology, and the cognition of the impact of fertilizer on the environment all had significant effects on the chemical fertilizer application behavior of grain farmers. Finally, according to the results of this study, some feasible suggestions are put forward.