Due to its larger ionic radius, further studies are needed before graphite can be used as an anode for sodium/potassium-ion batteries (SIBs/KIBs). It is believed that doping and increasing the layer spacing can improve the Na+/K+ storage. Herein, S/N co-doped graphite nanosheets (GNS) with an enlarged interlayer spacing of 0.39 nm were prepared via exfoliation with three-roll milling (TRM) combined with thiourea heated at different temperatures. This method generates abundant defects and active sites for GNS, as well as facilitates rapid access and transport of electrolytes and electrons/ions. The electrochemical results show that the S/N-doped GNS exfoliated 15 times and heated at 600 °C (SNGNS15-600) with thiourea as the electrode delivers a discharge capacity of 94 mAh g–1 over 6000 cycles at 10 A g–1 with an enhanced rate capability and stable performance for application in SIBs. Calculations using density functional theory show that the increased interlayer spacing by TRM and S, N co-doping enhances the adsorption energies of Na+ on graphite, thus improving the Na+ storage. As the anode for KIBs, the SNGNS15-600 electrode has a capacity of 142 mAh g–1 after 5000 cycles at 0.5 A g–1. This study provides an essential theoretical basis for the effective exfoliation of layered graphite-based materials and their applications in energy storage.