Post-translational modification (PTM) can affect the cognitive ability of animals. Lysinecrotonylation (Kcr) is a newly discovered post-translational modification widely found in organisms. Aipsmellifera is an important model for studying cognitive behavior in nature. Temperature is an important environmental factor affecting the development and health of bees. The results of this study show that low temperature exposure during the larval-pupa period will reduce the cognitive ability of adult worker bees, and the changes in the crotonylation modification level of worker bees with cognitive ability differences were analyzed in combination with LC-MS/MS technology and 4D proteomics technology. A total of 15,233 crotonylation modification sites were detected on 3017 proteins, of which two temperature-exposed samples with different lengths contained 402 modification sites on 304 proteins and 216 modification sites on 325 proteins. These proteins mainly functioned to participate in protein synthesis and energy metabolism related pathways. Parallel Reaction Monitoring (PRM) was used to verify the targeted quantification of protein synthesis and energy metabolism related to cognitive ability differences. This study elucidates the molecular basis for producing cognitive differences samples and provides a simple and easy-to-manipulate model for studying cognitive abilities.