To address the limitation of poor conductivity in composite bipolar plates (CBPs), a three‐dimensional (3D) conductive skeleton structure of graphite flakes (GF) is constructed using the sacrificial template method. This method prepares 3D polybenzoxazine/graphite flakes composite bipolar plates (3D‐PBA/GF CBPs) with high conductivity through vacuum impregnation of benzoxazine resin (BA). In this paper, the effect of the presence of a conductive network structure on the key properties of CBPs is analyzed, and the performance of GF randomly dispersed CBPs obtained through traditional solution dispersion is also compared. Thanks to the efficient conductive path within its 3D conductive skeleton structure, the 3D‐PBA/GF CBP achieves excellent conductivity meeting US Department of Energy (DOE) targets (in‐plane conductivity greater than 100 S/cm, area‐specific resistance less than 10 mΩ cm2) at a low filler content (50 wt%). In addition, CBPs with 3D conductive skeleton structures also exhibit qualified service performances to meet the requirements of proton exchange membrane fuel cells (PEMFCs). Compared with GF randomly dispersed CBPs, 3D‐PBA/GF CBPs exhibited higher power density in a single cell. This study demonstrates that constructing PBA/GF CBPs with a 3D conductive skeleton to achieve an accumulation distribution of conductive fillers is an efficient method for enhancing the conductivity of CBPs.