We developed building taxonomy for the Eastern Himalayas and estimated the distribution of building types in each town based on a field survey and local census data. We built a structure vulnerability model and mortality vulnerability model for each building type and simulated the loss distribution based on an earthquake scenario and probabilistic seismic hazards. Our seismic risk model indicates that the Eastern Himalayas have a regional annual average loss (AAL) of approximately 19 million RMB, which accounts for 0.02% of the 2018 regional gross domestic product (GDP). The AAL of reconstruction area covers nearly 7000 m² and the AAL of casualty is approximately 60 people. The city center of Lhasa contributes more than one-fifth of the economic AAL and 18% of the AAL of reconstruction area among the towns in this area, and the casualty risk is also the highest. Reinforced concrete building classes with less than three stories and unreinforced masonry contribute to most of the AAL in the study area. The AAL of Cuona County accounts for more than 0.35% of its annual GDP, which implies that it faces the most serious risk of damage by seismic disasters.