A novel soft template approach with agarose as carbon source has been developed for preparation of three-dimensional (3D) skeleton carbon coated Na3V2(PO4)3 (NVP/C) with controlled particle size of 20–200nm, as a cathode material of sodium ion battery with high performance. At 1C, the discharge capacity of as prepared cathode material is in the proximity of 113mAh/g, which is very close to its theoretical capacity (117mAh/g). Even at 50C, the discharge capacity can still maintain about 60mAh/g. After cycling 8000 times at 2C, the capacity retention is 87.5%. The electrochemical analysis and materials characterization reveal that the structure of NVP nano-particles coated with 3D-skeleton-carbon greatly improve the electrical conductivity of the electrode material, which endow sodium ion batteries with high capacity, high coulombic efficiency, long cycle life and great high rate performance. This novel template method provides a solution for one pot synthesis of size-controlled target materials with 3D-skeleton-carbon structure.