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.