Inorganic ions are indispensable substances in living systems, and are widely involved in many essential biological processes. Increasing evidence has shown that the disruption of ion homeostasis is closely related to health problems; thus, the in situ evaluation of ion levels and monitoring their dynamic changes in the living body are critical for precise diagnosis and therapy of diseases. Currently, along with the development of advanced imaging probes, optical imaging and magnetic resonance imaging (MRI) are becoming two major imaging approaches for the identification of ion dynamics. In this review, the design and fabrication of ion-sensitive fluorescent/MRI probes are introduced from the perspective of imaging principles. Furthermore, the recent advances in dynamic imaging of ion levels in living organisms, as well as understanding of ion dyshomeostasis related progression and early diagnosis of diseases, are summarized. Finally, the future perspectives of state-of-the-art ion-sensitive probes for biomedical applications are briefly discussed.