The Bangladesh, India and Myanmar (BIM) region has subtropical and tropical monsoon climates. Floods frequently occur around here. Assessing the flood risk in BIM region is important for the safety construction of the BCIM-EC. Based on datasets of precipitation from 1980 to 2016, river network, elevation, land use and etc., we selected ten indexes, namely, rainy season rainfall, rainstorm days, elevation, slope, drainage density, vegetation coverage, soil erodibility, population density, GDP, and land use. A comparative study of flood risk in BIM region is presented using the analytic hierarchy process (AHP) and the AHP_entropy methods. Based on the assessed results, about 1.05% and 28.76% of the BIM region have high risk and moderate to high risk. High risk zones in the BIM region were primarily concentrated on the Ganges Plain in northern India, Assam State in northeastern India, most of Bangladesh and southern Myanmar. Bangladesh is the country with the highest risk among three countries. The results show that high risk areas and moderate to high risk areas take up 10.61% and 65.87% of the total area of Bangladesh, respectively. Comparisons between results from AHP and AHP_entropy show that the latter yields a wider range of high flooding risk than the former. The study could provide an effective method for other neighboring countries of China in estimating the flood hazard areas, which can promote the construction of the BCIM-EC.