A series of microporous defective HKUST-1 materials (DMT-HK-nF) are synthesized employing varying amounts (n = 10, 30, and 50 wt%) of 3,5-dinitrobenzoic acid (DNBA) and 1,3,5-benzene tricarboxylic acid as linkers. Subsequently, stepwise washing and solvent exchanges are conducted to enhance the density of Cu(I) sites and increases the surface area. DMT-HK-30F exhibits superior H2 storage capacity (2.55 wt% at 77 K, 100 kPa and 0.93 wt% at 298 K, 7 MPa), approximately 41% and 48% higher compared to pristine HKUST-1 (1.82 wt% at 77 K, 100 kPa, and 0.63 wt% at 298 K, 7 MPa), respectively. This improvement is attributed to an increase in Cu(I) sites and the introduction of linker defects. However, further addition of DNBA decreases the H2 storage capacity due to a reduction in Cu(I) sites and surface area caused by the formation of “missing metal cluster” defects. This study demonstrates that the simultaneous introduction of appropriate defects and high-density Cu(I) sites into the microporous structure is an effective strategy for enhancing the hydrogen storage performance of metal-organic frameworks.