With the promising advances in nanomedicine, numerous strategies have emerged for the diagnosis and treatment of diseases. Among them, enzyme-based multifunctional nanocomposites have attracted a great deal of attention in the field of catalytic biomedicine. These nanocomposites with high catalytic activity are capable of converting low/non-toxic substances into therapeutic ones, thus realizing highly efficient, site-specific therapy with minimal side effects. Enzyme-based nanocomposites for catalytic biomedicine are mainly divided into three types: (i) natural-enzyme based nanocomposites; (ii) artificial-nanozyme based nanocomposites; and (iii) nanocomposites of natural-enzymes and nanozymes. In this review, we discuss key aspects of enzyme-based catalytic biomedicine, including the construction of enzyme-based nanocomposites, their unique properties and applications in catalytic biomedicine. We also highlight the main challenges faced in this field, and provide relevant guidelines for the rational design and extensive application of enzyme-based nanocomposites from our point of view.