Abstract Multi-energy (10–50 keV) boron difluoride (49BF2+) ions are implanted at a dose of 1015 cm−2 in the fused silica substrate to form a thin layer structure with a thickness of about 120 nm. The refractive index of fused silica substrate increases as a result of BF2 implantation, which applies to optical waveguide fabrication. Moreover, the absorption spectrum of the implanted sample shows two absorption peaks in the photon energy range from 4.0 eV to 6.52 eV, which are likely resulted from the B2β, oxygen divacancy and surface E′ center defects. The sample is thermally poled at the conditions of 5 kV, 60 min, and different temperatures, and the second-harmonic (SH) signal is measured using the Maker fringe technique. At low and moderate poling temperatures, the implanted and non-implanted samples have the same trend of SH signal variation with poling temperature (both increases first, and then reaches a maximum saturation value), and these signals have equivalent strength. At high poling temperature, the SH signal of the implanted sample is enhanced continuously, but the SH signal of the non-implanted sample is attenuated. The charge migration model of mobile ions can qualitatively explain the generation mechanism for second-order optical nonlinearity (SON) of the poled sample. The multi-energy BF2 ion implantation is found, for the first time, that it can enhance about 1.7 times of the SH signal of thermally poled fused silica glass at a high poling temperature.