At present, there is no clear consensus on the impact of carbohydrate feeds on bee colony health, and comprehensive research and evaluation in this context is lacking. To comprehensively and objectively examine the health status of honeybees after consuming those carbohydrates from multiple perspectives, experimental techniques, including high-throughput sequencing of the transcriptome, proboscis extension reflex (PER), and measuring bee growth parameters were employed. This study showed that compared with honey, feeding high fructose syrup (HFS) resulted in a decrease in the survival rate and body weight of bees, while sucrose decreased the learning and memory ability of bees. After feeding on honey, the main antimicrobial peptides including abaecin, apidaecin1, hymenoptin, and defensin in bees, are all upregulated in expression. The 14 DEGs significantly enriched in the axonal regeneration pathway were all downregulated in the sucrose group and HFS group. This study demonstrated that the expression of multiple genes involved in oxidative phosphorylation was downregulated in bees fed with HFS, moreover, HFS also affected the biosynthesis of unsaturated fatty acids. These effects may lead to energy and metabolic disorders (including fatty acids), thereby inhibiting the growth and development of bees. Sucrose can decrease the learning and memory ability of bees, which may be due to the downregulation of genes related to learning and memory in the axonal regeneration pathway. Honey can upregulate antimicrobial peptides and other immune-related proteins, activating the bee's immune system and boosting bees' immunity to pathogens.