Electrochemical hydrogen compressors (EHC) are favored for their quiet operation, efficiency, and low energy consumption in hydrogen purification and compression. A key challenge in EHC development is developing high-performance proton exchange membranes (PEMs) that manages water effectively. Herein, we've crafted a series of comb-shaped N-alkylation sulfonated poly(oxindole biphenylene) (SPOBP-Cn-x) (n = 0, 6, 10, 16) PEMs with varying side chain lengths. These PEMs feature distinct designs with sulfonic acid groups and hydrophobic chains attached to different locations of the indigo groups, which not only enhance ion conductivity by inducing the formation of microphase separated morphology but also retain their water absorption behaviors. The SPOBP-C10-10 membrane displayed the highest proton conductivity of 209.7 mS/cm (60 °C) and retain water uptake of 148.8 wt%. All the membranes exhibited low hydrogen back-diffusion permeability. Moreover, SPOBP-Cn-10 membranes outperformed Nafion 112 in EHC cells, with SPOBP-C10-10 exhibiting a notably low 0.1 V operating voltage at 1 A/cm2 (RH = 100%). EHC device durability tests for SPOBP-C10-10 at 200 mA/cm2 and 60 °C demonstrated a stability for over 440 hours with very slight variations in voltage. These results indicate that the comb-shaped structure with alkyl side chains and sulfonic acid groups adjacent to the backbone is an effective strategy for achieving satisfactory high conductivity, water uptake and energy efficiency of PEMs for use in EHC.