Abstract: The evaluation on biodiversity conservation of ecosystem had been paid much attention extensively, because it was the basis of the supporting function of ecosystem, yet the methodology for it remained an obsession in scientific community. In this paper, the animal species diversity conservation value of desert ecosystem in China was calculated based on the emergy theory proposed by H. T. Odum. And the added value due to species scarcity by means of endangered species index, referring to the species endangerment criteria of the International Union for Conservation of Nature and Natural Resources (IUCN), was evaluated. The results showed that the total animal species diversity conservation value of desert ecosystem in China was 3.51×104 billion yuan RMB, of which scarcity value was 3.64×103 billion yuan RMB. Among the total value,the mammal conservation value accounted for 52.41% and the bird conservation value accounted for 42.04%. The results indicated that desert ecosystem was providing huge value on the animal species diversity conservation, with increasing trends from east to west and south to north. In terms of regions, Xinjiang was the highest province of conservation value reaching up to 2.20 ×104 billion yuan RMB; Qinghai, Tibet, Inner Mongolia and Gansu are not much difference; and Shaanxi, Shanxi, Hebei, Jilin, Heilongjiang and Liaoning are lower regions in conservation value.