High-capacity metal–organic framework materials is constrained by their poor electron transport and unstable in aqueous. Herein, a spherical cobalt–nickel-based metal–organic framework (CoNi-MOF) micro-architecture with 18-π aromatic electron system of nickel phthalocyanine (NiPc) nanorods has been designed. In this system, intermolecular hydrogen (H) bonds between O in CoNi-MOF and H in nickel phthalocyanine (NiPc), along with longitudinal π-π stacking structure, could improve electron transport and structuralstability of MOFs. Benefiting from the 3D electron transport highways and “locking” effect of H bonds along with longitudinal π-π stacking structure, the optimized CoNi-MOF@NiPc electrode exhibits remarkable specific capacity of 807.365C g−1 at current density of 1 A/g, along with great cycling stability with 96.19 % capacity retention after 5000 cycles at 5 A/g, which is superior to the individual components. Besides, CoNi-MOF@NiPc//AC hybrid supercapacitor has been fabricated, which displays a maximum energy density of 130.68 Wh kg−1 at 962.09 W kg−1 and excellent cyclability (93.58 % capacity retention after 10,000 cycles). This study opens a new avenue for the design of organic electrodes and provides a new insight into H bond and π-π stacking structure effect toward advanced energy storage materials.