Layered double hydroxides (LDHs) with abundant accessible active sites are promising electrode materials for hybrid supercapacitor (HSC) due to their ultrahigh theoretical capacitances. However, the structural agglomeration of LDH leads to poor rate capability and durability. Herein, we construct a diffusion-controlled interface in hierarchical architecture of metal-organic framework (MOF) HKUST-1@cobalt-nickel LDH (denoted as HKUST-1@CoNiLDH) through an in situ etching/electro-deposition strategy. The rapid charge transfer and ionic diffusion in HKUST-1@CoNiLDH deliver a remarkable specific capacity of 297.23 mAh·g⁻¹ at 1 A·g⁻¹, superior to mostly reported LDH-based electrodes. More importantly, the as-prepared HKUST-1@CoNiLDH//activated carbon HSC exhibit a high energy density of 39.8 Wh·kg⁻¹ at a power density of 799.9 W·kg⁻¹ with an outstanding capacitance retention of 90% after 5,000 charge–discharge cycles. The in-depth understanding of the ionic diffusion among the MOF/LDH interfaces will greatly promote the further development of designing and synthesizing high performance energy conversion and storage devices.