Sodium-based dual-ion batteries (Na-DIBs) show a promising potential for large-scale energy storage applications due to the merits of environmental friendliness and low cost. However, Na-DIBs are generally subject to poor rate capability and cycling stability for the lack of suitable anodes to accommodate large Na+ ions. Herein, we propose a molecular grafting strategy to in-situ synthesize tin pyrophosphate nanodots implanted in N-doped carbon matrix (SnP2O7@N-C), which exhibits a high fraction of active SnP2O7 up to 95.6 wt% and a low content of N-doped carbon (4.4 wt%) as the conductive framework. As a result, this anode delivers a high specific capacity ∼400 mAh g−1 at 0.1 A g−1, excellent rate capability up to 5.0 A g−1, and excellent cycling stability with a capacity retention of 92% after 1200 cycles under a current density of 1.5 A g−1. Further, pairing this anode with an environmentally friendly KS6 graphite cathode yields a SnP2O7@N-C||KS6 Na-DIB, exhibiting an excellent rate capability up to 30 C, good fast-charge/slow-discharge performance, and long-term cycling life with a capacity retention of ∼96% after 1000 cycles at 20 C. This study provides a feasible strategy to develop high-performance anodes with high-fraction active materials for Na-based energy storage applications.