The baseline survey and detailed analysis of wildlife resources constitute an important basis and guidance for better conservation of both marine and island ecosystems. Birds and small mammals of Xisha Islands were surveyed in Woody Island and Lincoln Island by using line transects from April 2018 to December 2019, species composition and diversity differences compared with historical records were analyzed. Three species of small mammals were recorded in this survey, of which, Suncus murinus was common in forests and shrubs, whereas Rattus norvegicus and R. flavipectus were usually trapped near houses and villages. A total of sixty-five bird species of thirteen orders, twenty-six families were recorded in Xisha Islands, including twenty-nine newly recorded species, four kinds of national second-class protected animals. In terms of faunal distribution, a total of thirty-four species of birds are widespread species, twenty are Palaearctic species, and eleven are Oriental species. In terms of residence type, twenty-eight species of birds are winter visitors, twenty-three are residents, six are passage migrants, five are summer visitors, and three are vagrant visitors. In Lincoln Island, bird species richness was higher than Woody Island, but the diversity index and evenness index were lower. Bird species richness, diversity index, and evenness index in the rainy season were higher than those in the dry season. Much attention should be paid to Lincoln Island because there are more than one hundred thousand individuals of Sula sula inhabited in the forest, which is its only large breeding ground in China. Compared with the historical data published in 1974 and 2005, species richness of birds, especially the resident bird species has increased. These results suggest that, in Xisha Islands, small mammals have a low species richness, mainly distributed in the forest and near houses, and their community dynamics are mainly related to human activities, the related ecological effects should be investigated continuously and paid attention to prevent rodent damage. The bird community in Xisha Islands is characterized by high species richness, a major proportion of migratory birds, great differences between islands, seasons, and years, an increasing species number of resident birds, and the only large breeding ground for S. sula in China. As an important transfer station of migratory birds and a key habitat of S. sula, the integrity of the ecosystem in Xisha Islands is crucial for both the migratory birds and resident birds, especially S. sula, local conservation should be given extra attention.