Glyphosate (GY) is the most widely used herbicide in agriculture worldwide. Lead is a common heavy metal in the natural environment. Honeybees, as pollinators, are exposed to these pollutants. So far, few reports have evaluated the toxic effects of GY mixed with heavy metals on honeybees (Apis cerana cerana). This study found that the acute toxicity of lead (LC50 = 1083 mg/L) is much greater than that of GY (LC50 = 4764 mg/L) at 96 h. The acute toxicities of the mixed substances were as follows: LC50 = 621 mg/L of lead and LC50 = 946 mg/L of GY. The combination of lead and GY was more toxic than either of the individual substances alone. Compared to the individual toxicity, combined treatment significantly affected the bees’ learning and cognitive abilities and changed the relative expression of genes related to immune defense and detoxification metabolism in A. c. cerana. The combination of lead and GY seriously affected the behavior and physiology of the studied honeybees. This study provides basic data for further research on the combined effects of GY and heavy metals on bee health. It also serves as a reference for effective colony protection.