Neodymium-doped yttrium fluoride crystal has emerged as one of the most valuable functional materials, and has thus become a research hotspot and shown promising application value in recent years. In this work, utilizing 460 keV H and 6.0 MeV C ions implantation, the damage behavior, lattice structure change, spectral, and electrical characteristics of the Nd:YLF crystal induced by electronic and nuclear energy loss were investigated, utilizing complementary characterization techniques (X-ray diffraction, hardness and elastic (Young’s) modulus, micro-Raman, absorption, fluorescence spectra, and I–V characteristic curve). Thus, the annealing effect on the waveguide properties and the surface damage of the samples was discussed. The fabricated waveguide structure shows potential application in highly sensitive optoelectronic sensors.