There are 65 species of mammals in the park, accounting for 74% of all mammal species in Taiwan. Among them, 16 species of medium and large mammals almost cover all medium and large mammal species of Taiwan. Most of them are located in Mabolasi Mountain, Xiuguluan Mountain, Dafenjian Mountain and Yufeng of Central Mountain Range, where the forest ecosystems are well preserved without much human interference.

There are about 233 species of native birds in the park, covering almost all resident birds in the forests of Taiwan, and there are 29 species of birds endemic to Taiwan. Different species of birds have different preferences for their habitats. Besides steere's liocichla, rufous-faced warbler, black-throated bushtit and other few species which can inhabit both natural forests or plantation forests, most other species inhabit the areas where the habitats are well preserved.

Due to the high elevation, there are only 46 species of reptiles, and among them, there are 31 species of snakes, 12 species of lizards and 3 species of turtles. Alishan turtle-designed snake, Sauter’s ground snake, and tree lizard account for most of the population, and they are mainly located along Southern Cross-Island Highway and Dongpu hot spring areas, where the elevation is lower.

There are 21 species of amphibians in the park, of which there are 3 species with tails, and they are hynobius arisanensis, hynobius sonani and hynobius formosanus, all endemic to Taiwan. There are 18 anura species, and bufo bankorensis, zhangixalus moltrechti and buergeria robusta are endemic to Taiwan. The areas along Southern Cross-Island Highway and Dongpu hot spring at a lower elevation are their main habitats.

There are 286 species of butterflies in the park, including 27 species of papilionaceae, 30 species of pieridae, 75 species of lycaenidae, 108 species of nymphalidae and 46 species of skippers, and they account for about 71.2% of all butterfly species in Taiwan. Along the ancient trails in the saddle of Tataka and between Batongguan and Dongpu, the terrain and sufficient food supply often attract a large number of butterflies. They form a "Butterflies Pathway" worthy of butterfly appreciation and academic studies.

The streams in the park are the upper reaches of rivers. There is much less man-made pollution, making the area a good environment for freshwater fish to thrive. 16 species of freshwater fish have been recorded. Hemimyzon taitungensis and rhinogobius gigas are endemic fish species found only in eastern Taiwan. Onychostoma alticorpus and spinibarbus hollandi are precious fish species distributed only in the streams in the east and south.