The Sino-Mongolian border region is an important exploration hotspot in the Asia-Pacific margin and hosts one of the three major porphyry Cu-Au-Mo mineralization belts in the world. Variations in the concentration and spatial distribution of Mo in the region can indirectly reflect the distribution of other minerals, such as copper; therefore, Mo has been widely used as a pathfinder element for geochemical prospecting for porphyry Cu deposits. However, comprehensive and integrated analytical studies of single elements (e.g., Mo) in the Sino-Mongolian border region are lacking. Therefore, this study collected 10,453 catchment sediment samples from the study region and analyzed 69 elements. The concentration of Mo in these samples ranged from 0.10 to 84.96 mg/kg, with a median and mean of 0.84 mg/kg (considered the geochemical background value) and 0.97 mg/kg, respectively. The factors influencing the Mo concentration and spatial distribution along the Sino-Mongolian border region were investigated in terms of geological background, climate, precipitation, mineral distribution, and exploitation history. Influenced by climate and precipitation, Mo in catchment sediments is solubilized and easily transported under the oxidizing effect of hypergenesis. Mo concentrations were low in forested areas along the Altai Mountains in the west and Da Hinggan Ling Mountains in the east. Sixteen high-concentration Mo areas (geochemical province/domain, > 1.07 mg/kg, > Q75%) that contained 46 Mo geochemical anomalies (> 1.24 mg/kg, > Q85%) were circumscribed in this study. These anomalous areas were mainly related to the widespread distribution of minerals, coal-forming strata, and black shale deposits in the region. Compared to previous studies, this study identified more concentrated geochemical anomaly areas with a wider distribution in the Sino-Mongolian border region and provided higher quality geochemical data to promote further mineral exploration and support environmental change studies in this area.