© 2020 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim Structural modulation endows electrochemical hybrids with promising energy storage properties owing to their adjustable interfacial and/or electronic characteristics. For MXene-based materials, however, the facile but effective strategies for tuning their structural properties at nanoscale are still lacking. Herein, 3D crumpled S-functionalized Ti3C2Tx substrate is rationally integrated with Fe3O4/FeS heterostructures via coprecipitation and subsequent partial sulfurization to induce a highly active and stable electrode architecture. The unique heterostructures with tuned electronic properties can induce improved kinetics and structural stability. The surface engineering by S terminations on the MXene further unlocks extra (pseudo)capacitive lithium storage. Serving as anode for lithium storage, the optimized electrode delivers an excellent long-term cycling stability (913.9 mAh g−1 after 1000 cycles at 1 A g−1) and superior rate capability (490.4 mAh g−1 at 10 A g−1). Moreover, the (de)lithiation pathways associated with energy storage mechanisms are further revealed by operando X-ray diffraction, in situ electroanalytical techniques, and first-principles calculations. The hybrid electrode is proved to undergo stepwise phase transformations during discharging but a relatively uniform reconversion during charging, suggesting an asymmetric conversion mechanism. This work provides a novel strategy for designing high-performance hybrids and paves the way for in-depth understanding of complex lithium intercalation and conversion reactions.