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Alicyclic polyimides (PIs) have excellent properties in solubility, mechanical strength, thermal property, etc. This study developed two types of alicyclic PI-based mixed matrix membranes (MMMs) for water/n-butanol pervaporation application, which have never been investigated previously. The fillers were hydrophilic SiO₂ nanoparticles. The synthesized PI was mixed with SiO₂ nanoparticles in DMAc to make the casting solution, and a liquid film was formed over PET substrate using doctor blade. A dense MMM was fabricated at 80 °C and further treated via multi-stage curing (100–170 °C). The prepared membranes were characterized by FTIR, TGA, FE-SEM, water contact angle, and solvent swelling. The trends of pure solvent swelling effects agree well with the water contact angle results. Moreover, the pervaporation efficiencies of alicyclic PI/SiO₂ MMMs for 85 wt% n-butanol aqueous solution at 40 °C were investigated. The results showed that BCDA-3,4′-ODA/SiO₂ MMMs had a larger permeation flux and higher separation factor than BCDA-1,3,3-APB/SiO₂ MMMs. For both types of MMMs, the separation factor increased first and then decreased, with increasing SiO₂ loading. Based on the PSI performance, the optimal SiO₂ content was 0.5 wt% for BCDA-3,4′-ODA/SiO₂ MMMs and 5 wt% for BCDA-1,3,3-APB/SiO₂ MMMs. The overall separation efficiency of BCDA-3,4′-ODA-based membranes was 10–30-fold higher.