The Sanjiangyuan Region is an important component of the national ecological security strategic structure —“Two Screens & Three Zones”—in China, and its ecological security situation has a significant impact on China and even the region of Southeast Asia. Combined with information from field investigations and socioeconomic statistics, this paper adopts related methods of remote sensing parameter inversion, model simulation as well as the analytic hierarchy process and comprehensive index system to evaluate the ecological carrying capacity and ecological security situation of the Three River Sources Region. The results show: (1) the ecological carrying capacity of the Three River Sources Region is at the medium level and presents a pattern of decrease from southeast to northwest; (2) the major constraint factors on the ecological carrying capacity are water conservation quantity, NPP, surface water quality, vegetation coverage and the amount of threatened animals in the Three River Sources Region; (3) the general ecological security of the Three River Sources Region ranges from danger to arelatively safe situation; (4) the ecological carrying capacity is relatively low in the western underdeveloped region where the economic backwardness reduces the degree of local environmental protection effort; and meanwhile, the rapid population growth and the low cultural quality in more developed eastern region also causes conflict between economic development and environmental protection.