Taking the source regions of the Yangtze and Yellow Rivers as case and using both super-efficiency DEA and Malmquist DEA models, spatiotemporal changes in the eco-efficiency of grassland-based animal husbandry and its determinants were analysed. The results showed that there was a significant spatial difference in the eco-efficiency. In 2013, Yushu City, Chengduo County and Nangqian County experienced relatively high the super-efficiency, while Dari County, Maduo County and Tanggulashan Town were relatively low the super-efficiency. Based on the changes in space and time, the eco-efficiency was divided into three sequential stages:a steadily rising stage during the period 1994~2002, a differentiating stage during the period 2003~2006, and a rapidly rising stage during the period 2007~2013. It was further demonstrated that the eco-efficiency depended heavily on the technological progress and scale efficiency. And capital, precipitation and labor force were the determinants of the eco-efficiency. Therefore, increasing investment in science and technology; improving the technological and management level and labor quality; constructing water conservancy facilities, pastureland and livestock shelter; strengthening the protection of grassland ecosystem and frozen soil, will be most effective in the long term when they are complemented by appropriate public policies.