Second harmonic generation (SHG) is an important nonlinear process which is critical for applications, such as optical integrated circuit, nonlinear microscopy, laser, etc. Many challenges remain in the improvement of nonlinear conversion efficiency, since the typical value is of only 10−5 in nanostructures. Here, we theoretically demonstrate a periodic structure consisting of a lithium niobate (LN) bar and an LN disk, on a nanoscale (~300 nm) thin-film platform, which is proposed for a highly efficient SHG. By breaking the structure symmetry, a Fano resonance with a high Q, up to 2350 and a strong optical field enhancement reaching forty-two folds is achieved, which yields a high conversion efficiency, up to 3.165 × 10−4. In addition to its strong second harmonic (SH) signal, we also demonstrate that by applying only 0.444 V on the planar electrode configurations of the nanostructured LN, the wavelength of SH can be tuned within a 1 nm range, while keeping its relatively high conversion efficiency. The proposed structure with the high nonlinear conversion efficiency can be potentially applied for a single-molecule fluorescence imaging, high-resolution nonlinear microscopy and active compact optical device.