Bismuth based compounds are uniquely interesting as anode materials in energy storage devices such as rechargeable batteries, owing to their large volumetric capacity and suitable operating potential higher than graphite. How to achieve the high capacity durably and robustly remains an open challenge. To address this issue, here we propose a bio-inspired material engineering of yolk-shell composite that consists of bismuth sulfide (Bi2S3) nanowire assembly intimately encapsulated in polypyrrole (PPy) shell. The Bi2S3 yolk features a large void space and a short diffusion distance, while the PPy shell is highly conductive, flexible and resilient, allowing for the free volume variation upon ion uptake and release. When used as anode, the Bi2S3-PPy yolk-shell composite exhibits a superior Li storage cyclability (99% for 500 cycles) and a high rate capability (337mAhg–1 at 10C), outstripping any previous bismuth based materials. This composite also affords a high reversible capacity of 591mAhg−1 and a favorable durability for Na storage. The discrepancy between Li and Na storage may correlate to the larger volume change of Bi alloying with Na (∼250%) against with Li (~110%). This work offers a potential creative approach to engineering efficient electrodes for energy storage applications.