This paper proposes a novel intercalation approach to address the challenges of surface triboelectric charge dissipation and self-restacking of MXene layers in triboelectric nanogenerators (TENGs). The proposed strategy significantly improves the performance of TENGs, as it prevents the loss of surface charges and enhances the structural stability of MXene. First, the modified silica nanospheres (MSNs) of specific dimensions are synthesized, followed by their intercalation between MXene layers. This not only resolves the restacking issue but also dramatically increases the interlayer distance and MXene's surface area. The MSNs, acting as effective charge storage sites, significantly enhance surface charge density, whereas their high dielectric permittivity generates a synergistic effect that modulates the dielectric constant via polarization. Ultimately, the proposed MSN-intercalated MXene-based TENG demonstrates outstanding output performance (output voltage of ≈461 V, output current of ≈19 µA, and maximum peak power density of ≈691.2 µW cm−2) at a 2 wt.% MSN-intercalated MXene concentration. This study paves a new pathway for the structural design of tribonegative and charge storage layers in TENGs for energy harvesting.