It is widely believed that metacognition is a special cognitive capacity that only humans possess. A contentious debate in the field of comparative psychology is whether animals have metacognition. The exploration of this question has become an important way to uncover the phylogenetic roots of metacognition and to map the evolutionary history of higher cognitive functions in humans. This paper reviewed the main animal metacognition studies in the past 25 years. We summarize three common research paradigms and corresponding measures: the uncertainty monitoring paradigm, the information seeking paradigm, and the confidence judgment paradigm. Two opposing explanatory tendencies and their rationales are outlined in the field of animal metacognition research: the associative model and the metacognitive model. In response to the debate between the associative model and the metacognitive model, two future research orientations are proposed to improve the research paradigm to test the metacognitive model and the innovation theory to integrate the model.