Manure utilization in China is below optimum due to the inconsistency between farmers’ behavior and their intention to apply manure to their crops. With increasing constraints on the availability of chemical fertilizer and their impact on the environment, understanding how farmers’ perceptions affect their intention and behavior toward manure application is an issue for the implementation of sustainable agricultural development. This study uses primary survey data from 653 farmers. A probit model was used to assess the influence of cognition on farmers’ intentions, behavior, and the inconsistency between them in the use of manure application. Heterogeneity analysis was conducted to identify differences between farmers with different education levels and operation scales. The results showed that enhancing subjective norms, perceived behavioral control, and behavioral attitudes could increase their intention and behavior. Furthermore, improving the perceived behavioral control and behavioral attitudes of farmers would reduce the inconsistency between behavior and intention. In addition, some differences were identified in the role of farmers’ cognition with different education levels and operation scales. In general, it is necessary to enhance farmers’ comprehensive cognition of the value of manure through publicity and popularization of technology, reduce farmers’ perceptions about difficulties in applying manure through new policies and subsidies, and stimulate farmers’ enthusiasm to participate in the practice.
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