Based on the theory of population ecology, 971 national-level characteristic protection villages in the Yellow River Basin were regarded as one geographic population. Based on GIS spatial analysis and mathematical statistics method, the distribution dynamics and habitat selection characteristics of the population were clarified, and then the ecological factors affecting the distribution of this geographic population were revealed by comparing with geographic detectors. The result shows that: ① The distribution density of characteristic protection villages in the Yellow River Basin increased significantly with population growth, the distribution pattern changed from significant aggregation to insignificant dispersion with the increase of scale, and the distribution pattern evolved from multicenter to monocenter over time, but the agglomeration center was always located in the valley basin. ② The characteristic protection villages in the Yellow River Basin have the preferences of "gathering in the middle and low mountains, facing the sunny slope slopes, liking warmth and wetness, being close to the main stream of the Yellow River", and tend to be distributed in areas with medium population density and economically undeveloped areas. It is mainly located within 30 km along the national highway, 10 km along the provincial highway, 20～80 km around the center city, 60 km around the historic town, and 20 km around thetourist attractions and cultural preservation units. ③ The ecological factors influencing the population distribution of characteristic protected villages are comprehensive, non-equivalent and limited, and are dominated by cultural preservation units and altitude in the Yellow River Basin.