Inspired by natural catalytic compartments, various synthetic compartments that seclude catalytic reactions have been developed to understand complex multistep biosynthetic pathways, bestow therapeutic effects, or extend biosynthetic pathways in living cells. These emerging nanoreactors possessed many advantages over conventional biomedicine, such as good catalytic activity, specificity, and sustainability. In the past decade, a great number of efficient catalytic systems based on diverse nanoreactors (polymer vesicles, liposome, polymer micelles, inorganic-organic hybrid materials, MOFs, etc.) have been designed and employed to initiate in situ catalyzed chemical reactions for therapy. This review aims to present the recent progress in the development of catalytic systems based on nanoreactors for therapeutic applications, with a special emphasis on the principles and design strategies. Besides, the key components of nanoreactor-based catalytic systems, including nanocarriers, triggers or energy inputs, and products, are respectively introduced and discussed in detail. Challenges and prospects in the fabrication of therapeutic catalytic nanoreactors are also discussed as a conclusion to this review. We believe that catalytic nanoreactors will play an increasingly important role in modern biomedicine, with improved therapeutic performance and minimal side effects.