Flexible sodium-ion batteries are considered as the most promising flexible energy storage devices due to their bendability, low cost and high safety. However, the development of anode materials with high rate and long cycle stability is a key step in the development and application of flexible sodium ion batteries. Here, a simple vacuum filtration method is reported to obtain a bimetallic heterojunction structure. The heterojunction exhibits better performance than any single-phase material in sodium ion diffusion and storage. The results show that the electron rich Se site and the internal electric field generated by the electron transfer between cobalt selenide and nickel selenide in the heterojunction structure can provide abundant electrochemically active sites and effectively promote the electron transport in the process of sodiation/desodiation. The reversible capacity of NiCoSex/CG electrode obtained by heterojunction design is up to 338 mAh·g-1 at 0.1 A·g-1, and the capacity attenuation is ignorable at 2 A·g-1 for 2000 cycles. In addition, the assembled flexible full battery shows very good reversibility and output stability under bending and crimping. This idea of obtaining high performance anode of sodium ion battery by designing heterojunction structure can provide a new vision for the design and synthesis of other materials.