Plateau pika (Ochotona curzoniae) is a key species of alpine meadow ecosystem in Qinghai–Tibet Plateau. In this study, an observation and classification system of plateau pika disturbance intensity was constructed by multidimensional stereoscopic surveying, visual interpretation, geostatistics, principal component analysis, and clustering analysis, which can monitor and evaluate the disturbance of plateau pika activities comprehensively, scientifically, and efficiently in the head-water region of the Yellow River. The results show that (1) digital elevation model, digital orthophoto model, and three-dimensional real scene model can extract the surface morphology information changed by pika activities such as the number of pika holes and molehills, the area and volume of molehills, the elevation variation coefficient, the surface relief, and roughness; (2) The main load factors of the plateau pika disturbance intensity index (PPDII) are the surface roughness, the area and number of the molehills, and the number of mousehole; (3) The kappa value of PPDII clustering verification was 0.866, and the clustering analysis results were consistent with reality characteristics of plateau pika activity and distribution; (4) The disturbance in Laji Mountain is mainly slight and mild, accounting for 47.6% of sampling area, and the disturbance in Henan County is mainly medium and severe, accounting for 42.6% of sampling area. The results can provide reference data for the restoration and management of alpine meadow degradation in the head-water region of the Yellow River.