The design of an ultrabubble-repellent ion exchange membrane (IEM) with high ion transport efficiency for the electrolysis process remains an ongoing challenge. Herein, a multi-length-scaled heterogeneous ZrO2 coating was successfully introduced onto a sodium perfluorinated ion exchange membrane (SPIEM) surface by a facile coating method. Surface morphology optimization technology is developed to control the mesopore size, density and surface coverage of particles, thus forming a “popcorn-like” hierarchical micro/nanostructured ZrO2 coating (M-Ⅱ), which is conducive to bubble repellency in time and efficient ion transport. By using this membrane in chlor-alkali electrolysis, the power consumption can reach 2037.8 kWh t−1, representing reductions of 166.2 kWh and 113.2 kWh, respectively, for producing one ton of 100% NaOH compared with pristine SPIEM (2204 kWh t−1) and commercial Nafion TM N2030 (2151 kWh t−1) at 6 kA cm−2. As a result, M-Ⅱ can realize the production of sodium hydroxide and hydrogen at low cost. The M-Ⅱ also showed remarkable stability with negligible fluctuation for 360 h. Furthermore, after simple purification, the hydrogen from chlor-alkali electrolysis shows excellent performance in fuel cell tests. This study demonstrates the effectiveness of micro/nanoscale engineering on chlor-alkali electrolysis performance, providing a simple and efficient method for solving the gas adhesion problem in the electrolysis process.