In addressing the limitations imposed by the inherently low electronic conductivity and substantial ion transfer resistance of transition metal oxides (TMOs) in hybrid capacitive deionization (HCDI) applications, this study delineates a pioneering approach through the fabrication of a MoS2/MnO2 heterostructure, leveraging manganese dioxide (MnO2) as a model system. The investigation underscores the essentiality of constructing high-quality interfaces to act as conduits for directional charge flow, a critical but formidable challenge for enhancing desalination efficacy in electrode materials. By harnessing an atomistic “pump-driven” mechanism, the MoS2/MnO2 heterostructure demonstrably facilitates the promotion of desalination processes, underscored by the establishment of a potent local electric field (IEF) aimed at commanding charge dynamics. Empirical and computational analyses coalesce to unveil the preferential electron transfer from MoS2 to MnO2, a phenomenon precipitated by charge redistribution. This orchestrated charge flow not only augments electronic and ionic transfer efficiencies but also emboldens the MoS2/MnO2 heterostructure with enhanced desalination capabilities. The results show that MoS2/MnO2 demonstrates superior HCDI performance compared to MnO2 in a 500 mg L-1 NaCl solution at 1.2 V, with SRC of 33.21 mg g-1 and SRR of 1.50 mg g-1 min-1. The elucidation of this charge-guided dynamic, achieved through meticulous manipulation of the electronic microstructure and the IEF at the atomic scale, presents a novel paradigm for material science. This research presents an innovative approach for realizing robust charge-guided dynamics through the deliberate manipulation of the electronic microstructure and IEF of materials, employing an atomic-level “pump-driven” effect. This strategy opens new avenues for extending these principles to a broad array of advanced materials.