Sodium ion batteries have been considered a promising alternative to lithium ion batteries for large-scale energy storage owing to their low cost and high natural abundance. However, the commercialization of this device is hindered by the lack of suitable anodes with an optimized morphology that ensure high capacity and cycling stability of a battery. Here, we not only demonstrate that copper sulfide nanoplates exhibit close-to-theoretical capacity (~560 mAh g-1) and long-term cyclability, but also reveal that their sodiation follows a non-equilibrium reaction route, which involves successive crystallographic tuning. By employing in situ transmission electron microscopy, we examine the atomic structures of four distinct sodiation phases of copper sulfide nanoplates including a metastable phase and discover that the discharge profile of copper sulfide directly reflects the observed phase evolutions. Our work provides detailed insight into the sodiation process of the high-performance intercalation-conversion anode material.