The aim of this research was to compare the influence of modified lignin by ionic liquid (IL) on the physical and mechanical properties of wood-based panels bonded with urea-formaldehyde (UF) resin with the effect of glyoxalated lignin (GL) on UF properties. For this purpose, soda bagasse lignin was respectively modified by 1-ethyl-3-methylimidazolium acetate ([Emim][OAc]) IL and glyoxal and then the various content of modified lignins (10, 15, and 20%) were added at pH=7 during the UF resin synthesis instead of the second urea. The changes in the structure and thermal properties of lignin, after and before modification with glyoxal and IL, were analyzed by Fourier transform infrared spectrometry (FTIR) and differential scanning calorimetry (DSC). The physicochemical properties of the prepared resins as well as the water absorption, shear strength, and formaldehyde emission of the plywood panels made with these adhesives were measured according to standard methods. According to the FTIR spectra, the content of C=O bond increased in GL while in the IL-treated lignin the content of C-N bond markedly increased. DSC analysis indicated that lignin modified by IL had lower glass transition temperature (T-g) value compared to those modified with glyoxal and unmodified lignin, respectively. The UF resins containing IL-treated lignin exhibit a faster gel time compared to those prepared with GL. Equally, the plywood panels prepared with an IL had lower formaldehyde emission and higher mechanical strength compared to those made from UF resin containing GL. There were no significant differences in dimensional stability of the panels bonded with UFs modified with GL and those with IL-modified lignin.