Swift heavy ion irradiation has been widely used to modify refractive indices of optical materials for waveguide fabrication. In this work, we propose refractive index engineering by swift heavy ion (Ar) irradiation via electronic energy deposition to construct waveguides of diverse geometries in LiNbO3 crystal. The feasibility to modulate the refractive index of LiNbO3 crystal at variable depths through electronic energy depositions of argon ions at different energies has been experimentally explored. The surface and cladding-like optical waveguides with thicknesses of ~13, ~36 and ~23 μm have been produced by using swift Ar ion irradiation at single energy of ~120, ~240, and double energy of (120 + 240) MeV, respectively. The fabricated waveguides are capable of effective waveguiding in single and multiple modes at 1064 nm, which enables efficient guided-wave second harmonic generation at room temperature. This work paves the way to produce waveguides with diverse geometries in dielectric crystals through electronic damage of multiple swift heavy ion irradiation.