Photocatalytic upcycling of glycerol, a significant byproduct of biodiesel, to value-added lactic acid coupled with H2 production shows great promise for resource utilization and renewable fuel production. However, this reaction is currently limited to low efficiency and moderate selectivity due to insufficient light absorption, rapid charge carrier recombination, and unfavorable reaction kinetics. Herein, we report an atomic-level heterojunction photocatalyst consisting of CdxZn1–xS embedded uniformly with Cu–S3 moieties at the atomic-level scale. Due to the formation of a coherent-lattice interface with strong interfacial electronic interactions between Cu–S3 moieties and the CdxZn1–xS host, as well as the significant localized surface plasmon resonance effects induced by Cu–S3 moieties, such a photocatalyst shows much enhanced charge separation and transfer efficiency and strong light absorption covering the full solar-light spectrum. As a result, a 10-fold increase in glycerol conversion to lactic acid (LA) coupled with H2 production is achieved, with the selectivity of LA reaching over 95%. The present work demonstrates the potential of photocatalysis for biomass upcycling toward the coproduction of valuable chemicals and H2 fuel using structure-defined photocatalysts.