The development of Earth’s critical zone concept has strengthened the capacity of environmental science to better solve real-world problems, such as metal(loid) pollution in the remote alpine areas. The selected metal(loid) contents in soil, moss, and water were investigated to explore the geochemical distribution patterns, pollution levels, and potential ecological risks of metal(loid)s in the Shennongjia (SNJ) alpine critical zone of central China. The distribution of metal(loid)s in different spheres had horizontal and vertical differences. The maximum V, Ni, and Zn contents in water occurred at the sampling sites close to the Hohhot–Beihai Highway, while Dajiuhu Lake had the maximum Cu, Cr, and Mn contents. Most metal(loid) contents in the mosses showed an increasing trend from the northeast low-altitude area to the southwest high-altitude area, while As, Co, V, Ni, Cr, and Zn in soil decreased significantly with altitude and were enriched near the service areas and the highway. The contents of water Co and Ni, soil Cu and Mn, and moss As were evenly distributed and showed no significant differences with altitude. The enrichment factors, pollution index, Nemerow integrated pollution index, geo-accumulation index, heavy metal pollution index, contamination factor, and potential ecological risk index (PERI) were used to assess the pollution levels and ecological risks of SNJ soil, water, and atmosphere. The overall pollution levels of SNJ soil, moss, and water were low to moderate, low, and low, respectively. Soil V, Cu, Zn, moss As, Co, V, and Dajiuhu Lake water Mn were the main pollution factors. The ecological risks in the three spheres of the SNJ alpine critical zone were low to moderate, and As, Co, and V were the most critical potential ecological risk factors. The metal(loid)s pollution problem caused by the continuous development of tourism needs further attention.