Metal-organic frameworks (MOFs) hold great promise as porous materials for pervaporation applications. However, the exploration of MOF membranes in this field is still in its early stages. One of the main challenges is the relatively low mass flux and stability of pure MOF membranes compared to other materials used in pervaporation. In this study, we propose a novel approach to enhance the separation performance of MOF membranes for water and ethanol separation. Our strategy involves incorporating the 2,5-thiophenedicarboxylic acid (TDC) linker into the MOF-303 structure, partially replacing the 3,5-pyrazoledicarboxylic acid (PDC) linker. The goal is to increase the aperture size of the microporous channels in the pristine MOF-303 membrane, thereby improving the mass flux. X-ray diffraction characterization, combined with Rietveld refinement, confirmed that the partial substitution of PDC with TDC resulted in an increased pore-limiting diameter (PLD) of MOF-303. For instance, the pristine MOF-303 exhibited a PLD of 5.78 Å, while MOF-303(70/30) with 70% TDC replacement displayed a PLD of 6.02 Å. To fabricate the mixed-linker MOF-303 membranes, we utilized a seeded growth method, which yielded membranes with dense layers, as confirmed by scanning electron microscopy and air permeation characterization. The prepared membranes were subjected to pervaporation tests to evaluate their performance in separating 90 wt.% ethanol at 60 °C. The pristine MOF-303 membrane exhibited notable separation capabilities, with an average flux of 0.071 kg·m−2·hr−1 and a water/ethanol separation factor of 5371. Surpassing the unmodified MOF-303, the mixed-linker MOF-303(50/50) membrane demonstrated improved mass flux and water/ethanol separation factor. Specifically, the MOF-303(50/50) membrane displayed an average flux of 0.092 kg·m−2·hr−1 and a water/ethanol separation factor of 8500. Importantly, the unmodified MOF-303 membrane exhibited instability during prolonged pervaporation operation, whereas the mixed-linker MOF-303(50/50) membrane effectively addressed this issue. Further analysis using in situ Fourier transform infrared spectroscopy and water adsorption characterization revealed that MOF-303(50/50) possessed a strong affinity for water, comparable to the pristine MOF-303. Overall, our study highlights the potential of the mixed-linker approach to optimize the separation performance and stability of MOF-based membranes for pervaporation application.