Phase engineering of the electrode materials in terms of designing heterostructures, introducing heteroatom and defects, improves great prospects in accelerating the charge storage kinetics during the repeated Li+/Na+ insertion/deintercalation. Herein, a new design of Li/Na‐ion battery anodes through phase regulating is reported consisting of F‐doped SnO2‐SnS2 heterostructure nanocrystals with oxygen/sulfur vacancies (VO/VS) anchored on a 2D sulfur/nitrogen‐doped reduced graphene oxide matrix (F‐SnO2‐x‐SnS2‐x@N/S‐RGO). Consequently, the F‐SnO2‐x‐SnS2‐x@N/S‐RGO anode demonstrates superb high reversible capacity and long‐term cycling stability. Moreover, it exhibits excellent great rate capability with 589 mAh g−1 for Li+ and 296 mAh g−1 at 5 A g−1 for Na+. The enhanced Li/Na storage properties of the nanocomposites are not only attributed to the increase in conductivity caused by VO/VS and F doping (confirmed by DFT calculations) to accelerate their charge‐transfer kinetics but also the increased interaction between F‐SnO2‐x‐SnS2‐x and Li/Na through heterostructure. Meanwhile, the hierarchical F‐SnO2‐x‐SnS2‐x@N/S‐RGO network structure enables fast infiltration of electrolyte and improves electron/ion transportation in the electrode, and the corrosion resistance of F doping contributes to prolonged cycle stability.