Abstract Skyrmions—topologically protected chiral spin textures—are promising candidates for energy-efficient spintronics, yet their practical deployment has been hindered by challenges in achieving robust electric-field control and room-temperature stability. Here, we bridge this gap by demonstrating the realization of magnetic skyrmions stabilized at room temperature in ferroelectric lithium niobate (LiNbO₃). Crucially, these nanoscale quasiparticles exhibit an intrinsic multiferroic character, with ferroelectric polar nanodomains spatially colocalized at the core of each magnetic vortex. The skyrmions also enable dual electric- and magnetic-field tunability, allowing dynamic control over both their geometric parameters and topological states. This facilitates reversible transitions between distinct topological phases, including the transformation of Bloch-type skyrmions, Target Skyrmions, and Skyrmioniums. Remarkably, the excitation and manipulation of skyrmions profoundly optimize LiNbO₃'s ferroelectric properties: the detrimental DC-drift effect—a critical limitation in photonic modulators—is suppressed by over two orders of magnitude (from >10 dB/hour to <0.1 dB/hour), significantly enhancing device stability. Concomitantly, the skyrmion-induced ferroelectric ordering dramatically enhances the linear electro-optic response, yielding a record-high Pockels coefficient of 80 pm/V in thin-film modulators—a 150% enhancement over intrinsic LiNbO₃ (32 pm/V)—and enabling an ultra-low half-wave voltage of 0.63 V·cm. This work establishes a novel platform integrating topologically protected spin control, nonvolatile polarization, interface charge engineering, and photonic modulation, opening avenues for next-generation multifunctional magnetoelectric optical information technologies and corresponding high-speed photonic integrated circuits.