Lithium niobate (LN) is an excellent nonlinear optical material due to its large nonlinear coefficient, low loss, and broad optical transparency window. So, it is widely used in the generation of nonlinear harmonics. Magnetic toroidal dipole (MTD) resonance is a special optical resonance mode, which can effectively localize the light field inside the device, thus enhancing the nonlinear effects of the materials. In this work, we numerically study the second-harmonic generation (SHG) effect of the LN metasurface based on the MTD mode with a high quality factor (Q-factor). The designed LN nanorod dimer metasurface supports high Q-factor MTD guided mode resonances (GMRs), which are excited by varying the center spacing of the two nanorods, and the Q-factor can be controlled by the offset distance. The excited MTD can effectively confine the electric field within the device, which enables the LN metasurface SHG conversion efficiency to reach 1.15 × 10-2. In addition, by adjusting the structural parameters, it is possible to effectively modulate the wavelength and conversion efficiency of the SHG. Our results provide a new route for high-quality nonlinear light sources.