Hydrogenation or protonation provides a feasible pathway for exploring exotic physical functionality and phenomena within correlated oxide system through introducing an ion degree of freedom. This breakthrough provides great potential for enhancing the application of multidisciplinary equipment in the fields of artificial intelligence, related electronics and energy conversions. Unlike traditional substitutional chemical doping, hydrogenation enables the controllable and reversible control over the charge-lattice-spin-orbital coupling and magnetoelectric states in correlated system, without being constrained by the solid-solution limits. Our findings identify proton evolution as a powerful tuning knob to cooperatively regulate the magnetoelectric transport properties in correlated oxide heterojunction, specifically in metastable VO₂(B)/La_0.7Sr_0.3MnO₃(LSMO) systems grown via laser molecular beam epitaxy (LMBE). Upon hydrogenation, correlated VO₂(B)/LSMO heterojuction undergoes a reversible magnetoelectric phase transition from a ferromagnetic half-metallic state to a weakly ferromagnetic insulating state. This transition is accompanied by a pronounced out-of-plane lattice expansion due to the incorporation of protons and the formation of O—H bonds, as confirmed by X-ray diffraction (XRD). Proton evolution extensively suppresses both the electrical conductivity and ferromagnetic order in the pristine VO₂(B)/LSMO system. Remarkably, these properties recover through dehydrogenation via annealing in an oxygen-rich atmosphere, underscoring the high reversibility of hydrogen-induced magnetoelectric transitions. Spectroscopic analyses, including X-ray photoelectron spectroscopy (XPS) and synchrotron-based soft X-ray absorption spectroscopy (sXAS), provide further insights into the physical origin underlying the hydrogen-mediated magnetoelectric transitions. Hydrogen-related band filling in the d-orbital of correlated oxides accounts for the electron localization in VO₂(B)/LSMO heterostructure through hydrogenation, while the suppression of the Mn³⁺-Mn⁴⁺ double exchange leads to the magnetic transitions. This work not only expands the hydrogen-related phase diagram for correlated oxide system but also establishes a versatile pathway for designing exotic magnetoelectric functionalities via ionic evolution, which has great potential for developing protonic devices.