Recently, exploring appropriate anode materials for current commercial lithium-ion batteries (LIBs) with suitable operating potential and long cycle life has attracted extensive attention. Herein, a novel anode of Bi nanoparticles fully encapsulated in carbon nanosphere framework with uniform yolk–shell nanostructure was prepared via a facile hydrothermal method. Due to the special structure design, this anode of yolk–shell Bi@C can effectively moderate the volume exchange, avoid the aggregation of active Bi nanoparticle and provide superior kinetic during discharge/charge process. Cycling in the voltage of 0.01–2.0 V, yolk–shell Bi@C anode exhibits outstanding Li+ storage performance (a reversible capacity over 200 mAh g−1 after 400 cycles at 1.25 A g−1) and excellent rate capability (a capacity of 404, 347, 304, 275, 240, 199 and 163 mAh g−1 at 0.05, 0.1, 0.25, 0.5, 1.0, 1.8 and 3.2 A g−1, respectively). This work indicates that rational design of nanostructured anode materials is highly applicable for the next-generation LIBs.