Many animals (insects, fish, birds, rodents, etc.) can sense the geomagnetic field and use this information to orient and navigate in the natural world. However, the precise mechanisms by which animals sense the geomagnetic field information during magnetic orientation and navigation remain unclear. At present, scientists have also proposed a series of hypotheses of magnetoreception. While each hypothesis is supported by corresponding theoretical and experimental data, there is no hypothesis which can fully answer all the questions about animals in the process of magnetic orientation and navigation. This is mainly due to the diversity of species, and so animals may have evolved different magnetoreception mechanisms and orientation and navigation strategies. In order to deepen our understanding of animal magnetic orientation behaviors and magnetoreception mechanisms. First of all, we mainly elaborated on the widely recognized hypotheses of light-dependent radical-pair-based magnetoreception and light-independent magnetic particle-mediated magnetoreception, as well as the magnetite hypothesis based on blue light receptor protein Cryptochrome/iron-sulfur cluster assembly protein MagR magnetosensor protein complex and electromagnetic induction. In the second place, we analyzed the factors contributing to variations in magnetoreception mechanisms among different animal species during orientation and navigation, and the role of magnetic orientation and navigation in ecological behaviors such as animal migration, foraging and homing. Moreover, we discussed deeply how animals switch magnetoreception mechanisms to orient and navigate in different environments. Finally, we proposed the synergistic effect of the magnetoreception system and other sensory systems (such as visual, olfactory, auditory, etc.) in the process of magnetic orientation and navigation in animals. The purpose of this review is not only to enhance our understanding of animal magnetic orientation behavior and magnetoreception mechanisms, but also to improve our cognition of how animals utilize the geomagnetic field information for orientation and navigation in complex natural environments. Furthermore, we performed an in-depth analysis of the problems and challenges faced by the research field of animal magnetic orientation and navigation behavior and magnetoreception mechanisms. Based on this, we propose that the further research should strengthen interdisciplinary cooperation, especially the interdisciplinary integration with animal behavior, molecular biology, bioelectromagnetic, biophysics, neurobiology, and systems biology. This will help to promote the in-depth exploration and expansion of researches on magnetic orientation behavior and magnetoreception mechanisms. Simultaneously, through continuous exploration and innovation, it is expected to unveil more mysteries about animal orientation and navigation, and provide new ideas and methods for the development of ecological protection, biological navigation technology, and other fields.