Mountain channels have received relatively little study compared to lowland rivers due to their complicated fluvial geomorphology and inconvenient traffic. Classification schemes and habitat assessments in mountain channels should be strengthened to provide a scientific basis for river ecological restoration. Therefore, we tried to simplify the habitat assessment of mountain channels using a suitable habitat classification scheme based on high-resolution satellite imagery. We used China’s Chishui River basin because it is a typical mountain river system. Five parameters (stream order, elevation, slope, sinuosity and river network density) and 150 sites were used for habitat classification. In addition, we recorded 20 metrics in four categories (water environmental status, river morphology, riparian zone and human disturbance). Our results identified a total of 40 representative sampling sections belonging to six habitat types that were useful for habitat assessment across the Chishui River basin. The basin was given a mean comprehensive habitat quality index (CHQI) score of 130.66 ± 24.14 and classified under the status “good.” However, the headwaters, Tongmin River, Tongzi River and Xishui River were disturbed by various human activities. We conclude that the process of developing and simplifying our habitat assessment systems can be regarded as a reference for biomonitoring in other mountain river systems. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.