In order to effectively promote the standardization of pesticide application by farmers and promote high-quality development of the aquaculture industry, based on a survey data of 1 194 farmers in six counties of three provinces in the Yellow River Basin, and applying the binary Probit model, this paper explored the influence of market incentives on the standardization of farmers’ pesticide application behaviors under the governmental regulation scenario, and analyzed the interactions between the market incentives and governmental regulations. Results show that: market revenue has no significant effects on farmers’ pesticide application behaviors, but under the regulation of government regulation, market revenue can significantly promote farmers’ standardized pesticide application behaviors; market trust has a significant positive effect on farmers’ standardized pesticide application behaviors, and under the regulation of guided government regulation, the effect of market trust on farmers’ standardized pesticide application behaviors is significantly enhanced; farmers’ standardized pesticide application behaviors is also affected by age, years of farming, farming scale, farm size and other factors. The influence of market incentives on farmers’ standardized pesticide application behaviors vary according to the region and the scale of farming. Accordingly, policy recommendations were made to build a synergistic governance incentive mechanism between the market and the government, to improve market regulation and quality certification mechanisms, to enhance the reputation of farm product quality, and to strengthen the dissemination of information and education on the use of veterinary drugs in social networks.