Molybdenum disulfide (MoS2) nanoflower was grown onto 3D graphene (3DG) by a simple hydrothermal method. Subsequently, Nitrogen doped graphene quantum dots (NGQDs) were decorated on the surface of MoS2 to further enhance the electrochemical performance through a one-step electrodeposition method. The NGQDs decorated MoS2 on 3DG (NGQDs@MoS2/3DG) is further employed directly as a binder free anode of sodium ion batteries (SIBs). NGQD@MoS2/3DG nanoarchitecture delivers a specific capacity of 638 mA h g−1 at 50 mA g−1, and an ultra-high first cycle coulombic efficiency of 85.4%. The outstanding Na+ storage properties of NGQD@MoS2/3DG was attributed to the synergistic effect among the conductive 3DG carbon matrix, MoS2 nanoflowers and decorated NGQDs. These results obtained potentially unveil a path for the development of excellent electrochemical performance with high initial coulombic efficiency of SIBs.