Considering that simultaneous detection of xanthine (XA) and hypoxanthine (HXA) has been proved to be a reliable and feasible method for assessing fish freshness, a novel electrochemical sensing platform based on the ZnIn₂S₄/UiO-66-NH₂ modified glassy carbon electrode (GCE) was constructed in this study for XA and HXA determination. X-ray powder diffraction (XRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), and Fourier transform infrared spectroscopy (FT-IR) were performed to exhibit the morphology and structural characteristics of ZnIn₂S₄/UiO-66-NH₂. The Brunauer–Emmett–Teller (BET) displayed that the introduction of UiO-66-NH₂ can improve the specific surface area of the hybrid. Besides, the electrochemical sensing performance of ZnIn₂S₄/UiO-66-NH₂ was evaluated by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). For simultaneously detecting XA and HXA, the fabricated electrochemical sensor shows wide linear ranges (0.025–40 µM and 0.3–40 µM) with low detection limits (0.0083 µM and 0.1 µM). This sensor also has 96–103% recovery in detecting XA and HXA content in large yellow croaker meat samples, demonstrating a promising application in the marine food industry.