Metal nanoparticles have drawn great attention in heterogeneous catalysis. One challenge is that they are easily deactivated by migration-coalescence during the catalysis process because of their high surface energy. With the rapid development of nanoscience, encapsulating metal nanoparticles in nanoshells or nanopores becomes one of the most promising strategies to overcome the stability issue of the metal nanoparticles. Besides, the activity and selectivity could be simultaneously enhanced by taking advantage of the synergy between the metal nanoparticles and the encapsulating materials as well as the molecular sieving property of the encapsulating materials. In this review, we provide a comprehensive summary of the recent progress in the synthesis and catalytic properties of the encapsulated metal nanoparticles. This review begins with an introduction to the synthetic strategies for encapsulating metal nanoparticles with different architectures developed to date, including their encapsulation in nanoshells of inorganic oxides and carbon, porous materials (zeolites, metal-organic frameworks, and covalent organic frameworks), and organic capsules (dendrimers and organic cages). The advantages of the encapsulated metal nanoparticles are then discussed, such as enhanced stability and recyclability, improved selectivity, strong metal-support interactions, and the capability of enabling tandem catalysis, followed by the introduction of some representative applications of the encapsulated metal nanoparticles in thermo-, photo-, and electrocatalysis. At the end of this review, we discuss the remaining challenges associated with the encapsulated metal nanoparticles and provide our perspectives on the future development of the field.