The nonlinear lithium niobate (LiNbO3), characterized by transparency across a broad spectral range from ultraviolet to mid-infrared, stands out as an ideal material for second-harmonic generation (SHG). The concept of bound states in the continuum (BIC) represents a non-radiative mode embedded within the radiation continuum, offering the capability to confine the electromagnetic field within the nanostructure. Here, we propose the design of a LiNbO3 metasurface utilizing the BIC mechanism to enhance SHG at fundamental wavelengths above 2 µm, which injects new thoughts into the field of integrated optics and on-chip photonics. Notably, we rigorously accounted for the influence of the side-wall angle θ and the corner rounding radius R of the LiNbO3 metasurface, which arises from fabrication tolerances. Considering those influences in the simulation, we achieved a quasi-BIC (q-BIC) with a quality factor (Q-factor) up to 1.44 × 105. Moreover, by considering the depleted pump model, the absolute efficiency of SHG reached 4.09% with a corresponding normalized efficiency of 8.19 × 10−10m2/W under a radiation intensity of 5 kW/cm2. Our research aims to establish a predictive framework through numerical simulations, specifically addressing realistic fabrication problems. This approach is intended to optimize the parameters for LiNbO3 metasurface fabrication, ensuring that the subsequent experiment efforts are efficient. Our findings provide an approach to predicting the optical response in actual structures and inspire new applications in photonics.