Electrical manipulation of skyrmions attracts considerable attention for its rich physics and promising applications. To date, such a manipulation is realized mainly via spin-polarized current based on spin-transfer torque or spin–orbital torque effect. However, this scheme is energy consuming and may produce massive Joule heating. To reduce energy dissipation and risk of heightened temperatures of skyrmion-based devices, an effective solution is to use electric field instead of current as stimulus. Here, we realize an electric-field manipulation of skyrmions in a nanostructured ferromagnetic/ferroelectrical heterostructure at room temperature via an inverse magneto-mechanical effect. Intriguingly, such a manipulation is non-volatile and exhibits a multistate feature. Numerical simulations indicate that the electric-field manipulation of skyrmions originates from strain-mediated modification of effective magnetic anisotropy and Dzyaloshinskii–Moriya interaction. Our results open a direction for constructing low-energy-dissipation, non-volatile, and multistate skyrmion-based spintronic devices.