Single-atom catalysts provide efficiently utilized active sites to improve catalytic activities while improving the stability and enhancing the activities to the level of their bulk metallic counterparts are grand challenges. Herein, we demonstrate a family of single-atom catalysts with different interaction types by confining metal single atoms into the van der Waals gap of two-dimensional SnS2. The relatively weak bonding between the noble metal single atoms and the host endows the single atoms with more intrinsic catalytic activity compared to the ones with strong chemical bonding, while the protection offered by the layered material leads to ultrahigh stability compared to the physically adsorbed single-atom catalysts on the surface. Specifically, the trace Pt-intercalated SnS2 catalyst has superior long-term durability and comparable performance to that of commercial 10 wt% Pt/C catalyst in hydrogen evolution reaction. This work opens an avenue to explore high-performance intercalated single-atom electrocatalysts within various two-dimensional materials.