Hydrogenases, as a class of highly efficient and reversible biological catalysts, can catalyze the reduction of protons to molecular hydrogen, thus demonstrating great potential in a wide range of fields such as renewable energy production and green chemistry. Despite their significant potential, the large-scale industrial application of hydrogenases has long been constrained by several inherent limitations, including high sensitivity to molecular oxygen, the challenges in the in vitro reconstitution and maturation of their catalytic centers, and the inefficiency and instability of the natural electron transfer pathways. To overcome these limitations and enhance the catalytic performance of hydrogenases, researchers have developed various strategies, among which enzyme molecular engineering, photo-driven modification, and enzyme immobilization techniques are the most common exploration directions. Particularly, enzyme immobilization technology is widely used to improve the reusability of hydrogenases, but traditional immobilization methods often come with disadvantages in practical applications, such as complex multi-step procedures and insufficient biocompatibility of the immobilization materials. In recent years, bioencapsulation technology has emerged as a promising alternative strategy to enhance the catalytic performance of hydrogenases. This method utilizes biologically derived encapsulation materials to construct physically confined and precisely defined chemical microenvironments around the enzyme molecules, offering simpler self-assembly processes and superior biocompatibility. With these biomimetic constructs, bioencapsulation technology not only provides better oxygen tolerance but also helps to create a local microenvironment conducive to sustained catalytic function. This article systematically reviews the latest research progress of two main bioencapsulation strategies for hydrogenases: one is the encapsulation technology based on protein-based nanocages; the other is the engineering strategy for whole-cell hydrogenase expression. In the nanocage-based systems, this article focuses on the structural and functional characteristics of virus-like capsids and carboxysome protein shells, which serve as efficient enzyme encapsulation scaffolds, not only providing a stable physical barrier to prevent oxygen diffusion but also enabling high-density enzyme loading, thereby promoting substrate channeling effects and electron transfer kinetics. This article also discusses whole-cell encapsulation systems, which achieve hydrogenase compartmentalization within engineered cellular structures or by using external natural polysaccharide-based encapsulation matrices to wrap whole-cell catalysts. Bioencapsulation strategies can bring multiple synergistic benefits: they can effectively protect hydrogenases from oxygen-mediated inactivation, significantly delay the decline of catalytic activity over time, and enhance the hydrogen production rate by increasing the local concentration of active enzyme molecules and optimizing the electron transfer efficiency from redox partners to the catalytic center.Despite the significant progress made, several technical challenges remain to be addressed. The main obstacles include limited enzyme loading and encapsulation efficiency, insufficient long-term stability of encapsulation materials under operating conditions, and the need to improve the matching of the photo-biological interface in systems integrating light-harvesting components with enzymatic catalysis. Future efforts can focus on the integration of multiple technological approaches, such as using computer-aided protein design to optimize encapsulation structures, developing engineered electron transfer pathways to enhance catalytic conversion efficiency, and designing composite multifunctional materials with both structural stability and functional adaptability. These directions collectively aim to achieve efficient, stable, and scalable hydrogen production applications of bioencapsulated hydrogenase systems.