Metal based Prussian blue composite materials with heterogeneous structures possess substantial potential for enhancing both ionic and charge transfer processes, ultimately expediting electrochemical reaction kinetics for various battery devices. However, the limited bonding between carbon materials and Prussian blue analogues (PBAs) and the uncontrolled nucleation rate of metal component resulted in limited specific capacity and cyclic stability. Herein, we introduced a novel approach for the in-situ synthesis of Ni-PBA with an inverted-pyramid structure on a three-dimensional ultra-thin carbon frames (3DUC) substrate via a hydrothermal method. The inverted pyramid structure fits tightly with the 3DUC during nucleation to form a one-piece stable structure. This integration effectively curbs aggregation and hasty nucleation tendencies of NiPBA. Furthermore, the abundant voids and interconnected networks within the 3DUC structure significantly reduce ion diffusion path lengths, thereby lowering the Na diffusion barrier and enhancing the material’s capacitance contribution rate. Consequently, this cathode material exhibits commendable initial capacity (125.2 mAh/g at 50 mA g−1) and exceptional long-term cycling stability (with a capacity retention of 89.06 % after 900 cycles at 50 mA g−1). These findings hold significant promise for advancing the commercial viability of metal-PBA based electrodes by rational heterogeneous structure design.