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.