Photocatalytic water splitting is a commonly used pathway for hydrogen (H2) production, and it is crucial to develop highly active ZnIn2S4 (ZIS)-based photocatalytic systems. In recent years, metal-organic frameworks (MOFs) are also of great interest in the fields of energy production and environmental remediation. Therefore, this study primarily focuses on the fabrication of a series of heterojunction hexagonal prism-shaped Zr-based MOF@ZIS core-shell nanorods through a simple solvothermal method, in which ZIS nanosheets are highly distributed on the surface of the Zr-based MOF (NU-1000). The photocatalytic activities of the resulting materials were evaluated under visible light illumination (λ ≥ 400 nm) by combining different contents of NU-1000 with ZIS. The H2 evolution results demonstrate that the optimal content of NU-1000 corresponds to a photocatalytic H2 production rate of 8.53 mmol g−1 h−1, which is 5.3 times higher than that of pure ZIS. The enhanced photocatalytic activity of the NU-1000@ZIS (NUZ) heterojunction can be attributed to the incorporation of the NU-1000, which provides abundant active sites due to its larger specific surface area. Additionally, the well-matched band structure between the NU-1000 and ZIS is beneficial to efficiently transfer and separate the photogenerated charge carriers. Furthermore, the NUZ core-shell nanorods exhibit excellent stability, offering a new approach for the fabrication of composite photocatalysts by combining MOF-based and ZIS in the field of photocatalytic H2 production.