Fallowing is a crucial measure in relieving ecological resource pressure, safeguarding farmland, and propelling the advancement of modern agricultural practices. Based on a data from the China Rural Revitalization Survey (CRRS) and from the perspective of behavioral economics, this study analyzed the primary influencing factors of farmers’ fallowing behaviors and explored the heterogeneity across different ecological regions by the propensity score matching model and the binary Logistic regression model. Results reveal that 5.41% of farmers engaged in fallowing, with 47.93% being induced and 52.07% being spontaneous in their participation. Ecological subsidies significantly stimulated farmers’ fallowing behaviors in the induced category, while occupational path dependence and policy learning ability notably restrained farmers’ fallowing behavior in the spontaneous category. The impacts of ecological subsidies on farmers’ fallowing behavior varied across different ecological regions. While other factors exhibited significant heterogeneity. Therefore, to elevate the fallowing rate among farmers, this paper suggests: deepening the reform of the ecological subsidy system, adopting diversified ecological subsidy approaches, enhancing vocational training, reducing farmers’ reliance on land, and reinforcing education on fallowing policies to augment farmers’ awareness of policy.