Despite two‐dimensional (2D) conductive metal‐organic frameworks (cMOFs) being attractive due to their intrinsic electrical conductivity and redox activity for energy applications, alleviating the constrained mass transfer within long‐range micropore channels remains a significant challenge. Herein, we present a tandem assembly and etching chemistry, to incorporate perpendicularly aligned mesopores into the micropores of cMOF, via a bi‐functional modulator. Synchrotron spectral and morphological analyses demonstrate that the elaborate ammonia modulator first coordinates with Zn2+ forming defects during the initial self‐assembly of cMOF oligomers, which then initiates mesoporous cMOFs via in‐situ etching. In‐situ spectroscopy and theoretical simulations further reveal that such a unique perpendicular mesoporous structure shorts the micropore channels by two orders of magnitude and relaxes the inherent ion stacking within micropores, leading to five times faster Na+ transportation and a remarkable rate capability at 250 C and sodium storage lifespan over 50,000 cycles. Our protocol opens up a new avenue for introducing mesopores into microporous cMOFs for advanced energy applications and beyond.