Biopesticides are perceived as a feasible alternative to chemical pesticides, providing an effective approach to pest management while mitigating the undesirable effects of chemical pesticide overuse. Yet, due to the distinctive attributes of the two types of pesticides, farmers often adopt a combination of both. This study aimed to probe the interdependent relationship underlying the mixed use of chemical pesticides and biopesticides by farmers in the rice–crayfish integrated system (RCIS) in Hubei province, China. We also sought to identify influencing factors and associated consequences of this practice. Given that the adoption of chemical pesticides and biopesticides by farmers is not mutually exclusive, a multivariable probit model was utilized to estimate simultaneous pesticide applications. Survey data from 736 RCIS farmers revealed that 10.50% of the sample farmers employ a combination of chemical pesticides and biopesticides. A substitution relationship was observed between the adoption of chemical pesticides and biopesticides by farmers, whereas no significant complementary relationship was found in the application of the two types of pesticides. The primary motivation for the mixed use of pesticides by farmers is to achieve superior pest control efficacy. Notably, when integrating the use of pesticides, farmers pay less attention to factors such as resource endowments and multiple production objectives. Further analysis indicated that farmers display significant concern for pesticide attributes including insecticidal efficacy, toxicity, insecticidal spectrum, and validity period. The mixed use of pesticides has resulted in a decreased frequency of pesticide application but has escalated the cost. While the mixed use of pesticides elevated the selling price of rice, no significant improvement was observed in yield and output value. The insights garnered from this study offer strategic implications for policymakers on how to enhance the judicious adoption of pesticides by farmers.