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Simple Summary: Takins in the Eastern Himalayas of China are very diverse; however, species research in this region is lacking. Therefore, limited background data are available on the different subspecies present in this region. Using ecological models and surveys, this study examined the factors of two subspecies in this region, including phenotypic characteristics, population, activity, and distribution range, to provide species identification and classification references. The results revealed that the Mishmi takin and Bhutan takin could be differentiated using camera trapping. Their distribution areas, population densities, and population sizes could be determined in all human-accessible areas of the Eastern Himalayas in China. Thus, this study contributes to basic animal diversity knowledge and provides detailed information and references for species identification, distribution ranges, and population characteristics of the Mishmi and Bhutan takins. Moreover, this study provides resource data for subspecies classification that can be used to promote effective protection measures for endangered species. Limited background data are available on the Mishmi takin (Budorcas taxicolor taxicolor) and Bhutan takin (Budorcas taxicolor whitei) subspecies in the Eastern Himalayas of China because of the lack of systematic field investigations and research. Therefore, mature-animal ecological methods were used to evaluate these takin subspecies' phenotypic characteristics, distribution range, activity rhythm, and population size. From 2013 to 2022, 214 camera traps were installed for wild ungulate monitoring and investigation in all human-accessible areas of the Eastern Himalayas, resulting in 4837 distinguishable takin photographs. The external morphological characteristics were described and compared using visual data. Artificial image correction and related technologies were used to establish physical image models based on the differences between subspecies. MaxEnt niche and random encounter models obtained distribution ranges and population densities. Mishmi takins have a distribution area of 17,314 km2, population density of 0.1729 ± 0.0134 takins/km2, and population size of 2995 ± 232. Bhutan takins have a distribution area of 25,006 km2, population density of 0.1359 ± 0.0264 takins/km2, and population size of 3398 ± 660. Long-term monitoring data confirmed that the vertical migration within the mountain ecosystems is influenced by climate. Mishmi takins are active at 500–4500 m, whereas Bhutan takins are active at 1500–4500 m. The two subspecies were active at >3500 m from May to October yearly (rainy season). In addition, surveying combined with model simulation shows that the Yarlung Zangbo River is not an obstacle to migration. This study provides basic data that contribute to animal diversity knowledge in biodiversity hotspots of the Eastern Himalayas and detailed information and references for species identification, distribution range, and population characteristics. [ABSTRACT FROM AUTHOR]