As an essential element, magnesium is involved in a variety of physiological processes. Magnesium is the second most abundant cation in cells and the fourth most abundant cation in living organisms. Magnesium-based biomaterials are considered to be biocompatible and biodegradable, and they are promising for application in biomedicine. Among them, magnesium phosphates have attracted increasing interest in biomedical fields in recent years, because both magnesium and phosphorus are common elements in the human body. Magnesium phosphates exhibit many similar characteristics, such as excellent biocompatibility and pH-responsive degradability, to calcium phosphates that are widely applied in biomedicine. Magnesium phosphates are used in nanomedicine in the form of monodisperse particles, or used in tissue engineering in the form of cements, ceramics, scaffolds, coatings and so on. This review focuses on the state-of-the-art progress made in magnesium phosphate-based biomaterials and their biomedical applications, including nanostructured magnesium phosphates and magnesium phosphate-based cements, ceramics, scaffolds, coatings and so on. Finally, the challenges and future research directions of magnesium phosphate-based biomaterials are also explored.