Multiple van der Waals (vdW) gaps invoke abundant opportunities for contriving artificial architectures and tailoring desired properties via the intercalation route beyond the reach of conventional concepts. Intriguingly, the electrochemical intercalation strategy can precisely and reversibly tune the intercalation stage of charged functional species. This study presents a valid structural editing protocol facilitated by electrochemical intercalation to engineer MXene interlayers, ultimately incorporating in situ constructed carbon nanotube (CNT) electric bridges for enhanced ion storage and transport pathways. The method allows for the precise modulation of electrochemical forces to tailor materials for specific applications. Deep intercalation and in situ growth processes establish robust anchoring sites and connectivity hubs between MXenes and CNTs, ensuring structural homogeneity and stability in advanced electrode materials. The results demonstrate the effectiveness of electrochemistry-mediated interlayer nanoengineering in MXenes, offering a versatile approach to design vdW heterostructures with tailored functionalities for energy storage and conversion applications. This work highlights the potential of electrochemical modulation in advancing materials engineering strategies for next-generation energy storage technologies.