The development of noble-metal-free catalysts for upgrading biomass feedstocks to chemicals and fuels remains a crucial and challenging target. Catalytic hydrogenation of biomass-derived levulinic acid (LA) to γ-valerolactone (GVL) is one of the essential reactions for biomass valorization. Herein, we report a confined Cu cluster catalyst, Cu/NMSSs-NH2, in which ultrafine Cu nanoclusters are uniformly encapsulated in the channels of amino-functionalized nanosized mesoporous silica spheres (NMSSs-NH2). The surface amino functionalization of NMSSs plays a critical role in dispersing and stabilizing Cu species. The obtained Cu/NMSSs-NH2 affords an excellent LA hydrogenation performance, with a GVL yield as high as 98% achieved, much higher than that of unconfined Cu particles in pristine NMSSs (Cu/NMSSs, 42%). Comprehensive characterization studies including X-ray diffraction, transmission electron microscopy, and X-ray photoelectron spectroscopy reveal that the modified microenvironment of NMSSs could not only offer a confined space but also induce an electronic interaction between metal species and the support, which effectively restrains the Cu nanoclusters from aggregation. This study unlocks the potential of inexpensive Cu cluster-based catalysts for the hydrogenation of renewable biomass to high-value chemicals.