Magnesium ion batteries (MIBs) are promising for large-scale energy storage but limited by the poor diffusion kinetics of the cathodes. Hybrid ion batteries, which combine both the advantages of fast alkali metal ions intercalation cathode and dendrite-free Mg anode that exhibits satisfactory electrochemical performance, are an option. Herein, a novel NaTi2(PO4)3 nanowire clusters (NTP-NW/C) as hybrid magnesium-sodium ion batteries (MSIBs) cathode is presented for the first time. Combining the advantages of NTP nanowires and the homogeneous carbon skeleton, the novel 3D hierarchical structure endows short ion transport pathway, fast charge transfer speed and robust structure stability during sodiation/de-sodiation. As a result, the hybrid MSIB showed good electrochemical performances: a high reversible capacity of 124 mA h g−1 at 1 C, good rate capability (60 mA h g−1 at 10 C) and cycling stability (capacity retention of 97% after 100 cycles at 5 C). This novel design will be highly promising for large-scale energy storage applications.