Pollinators play an important role in ecosystems, but global climate change threatens the diversity and geographical distribution of pollinators. Bees are some of the most important pollinators and are particularly sensitive to climate change and environmental change. Apis laboriosa and Apis dorsata are two species of giant honeybees distributed in Asia, and play important roles in their ecosystems. In this study, we analyzed the key factors affecting the distribution of two species, as well as their potential suitable areas and possible co-existence regional changes under the global climate change. We collected and filtered global distribution data of A. laboriosa and A. dorsata, then used eight climatic variables and Community Climate System Model version 4 (CCSM4) to simulate their potential suitable areas for the past, present and future (using two different climate scenarios) using MaxEnt. Finally, we used ArcGIS 10.2 and ENMTools to calculate range overlap and niche overlap of the two species in order to infer areas of coexistence. Temperature-related variables had the largest contribution to the model simulation. Among these variables, temperature seasonality (Bio 4) and mean temperature of coldest quarter (Bio 11) showed the strongest influence on the distributions of two giant honeybees. Under the current climate scenario, the species overlap in Nepal and Yunnan of China, with low niche overlap index. Between the last-glacial maximum to the present both honeybees moved northwest to their present range. A. laboriosa is projected to move to the northeast and A. dorsata may move southeast. Only 6.6% of overlapping distribution is currently protected, and further work is needed to protect these key areas.