To better couple with commercial cathodes, such as LiCoO2and LiFePO4, graphite‐based composites containing a small proportion of silicon are recognized as promising anodes for practical application in lithium‐ion batteries (LIBs). However, the prepared Si/C composite still suffers from either rapid capacity fading or the high cost up to now. Here, the facile preparation of hierarchical graphene‐scaffolded silicon/graphite composite is reported. In this designed 3D structure, Si nanoparticles are homogeneously dispersed on commercial graphites and then uniformly encapsulated in the hierarchical graphene scaffold. This hierarchical structure is also well characterized by the synchrotron X‐ray computed nanotomography technique. When evaluated as anodes for LIBs, the hierarchical composite, with the Si weight ratio of 5 wt%, exhibits a reversible capacity of 559 mA h g−1at 75 mA g−1, suggesting an unprecedented utilization of Si up to 95%. Even at 372 mA g−1, the composite can still maintain a high capacity retention of 90% after 100 cycles. Coupled with the LiFePO4cathode, the full cell shows the high capacity of 114 mA h g−1at 170 mA g−1. The excellent Li‐storage properties can be ascribed to the unique designed hierarchical structure.