Tin disulfide (SnS2) with high theoretical capacity has been regarded as a promising candidate for sodium-ion capture, but it still encounters challenges of sluggish ion-storage kinetics and performance decay caused by its poor intrinsic conductivity and volume change. Here, we successfully address the aforementioned issues of SnS2 by synthesizing hollow ZnS/SnS2 microboxes embedded in sulfur-doped graphene (ZnS/SnS2@SG) through a macro (soft/hard interface) to micro (heterogeneous) interface engineering design. The resulting ZnS/SnS2@SG displays superior capacitive deionization (CDI) performance, including an impressive desalination capacity (109.7 mgNaCl g−1) with an ultrafast time-average desalination rate of 10.1 mgNaCl g−1 min−1 and attractive cyclic durability, outperforming most of the reported state-of-the-art CDI electrodes. The interface optimization of the surface structure and atomic-scale enhances the desalination performance, which can be decoupled into carbon substrate protection and charge rearrangement modulation, that is, graphene as a soft buffer layer alleviates volume expansion, and internal electric field induced by a uniform heterojunction lowers the Na+ diffusion energy barrier. Density functional theory calculations further confirmed that the uniform heterostructure facilitates the adsorption of Na+ and spontaneous electron transfer, thus achieving high electrochemical performance. The interface engineering strategy showcased in this work exhibits great potential in guiding material innovations for next-generation electrochemical ion capture.