Soil animals play important roles in conservation of soil health. Their diversity can sensitively reflect soil disturbances caused by human activities and climate change and they also influence the above-ground ecosystem through interactions with other below-ground components. Inadequate knowledge on taxonomy of soil animals as well as the complexity of soil food web greatly limit the research on the links between soil animals and soil health. We here review recent advances in soil animals as indicators of soil health, point out the significance of soil animals and soil food webs in maintenance of healthy soil, and propose to improve the establishment of genome and functional traits database. Soil health assessment that integrates the diversity of soil animals, functional traits and soil food web structure is thought to be most promising.