In this study, ionic liquid-modified polyethylene terephthalate was prepared for the first time via the condensation copolymerization of 1,3-bis(2-hydroxyethyl) imidazolium chloride (tetrafluoroborate, hexafluorophosphate) with dimethyl terephthalate and ethylene glycol using stannous chloride as the catalyst. The obtained functional materials were characterized using viscosity, infrared spectra, thermogravimetric analysis, scanning electron microscopy, and conductivity measurement. The wettabilities of the materials with different counterions were also tested by static water contact angle measurement. The results revealed that both the thermal stability and the hydrophilicity of functional material were enhanced greatly due to the introduction of ionic liquids. In addition, the antibacterial performances of the copolymers were also evaluated by in vitro assay, and the results proved that the ionic liquid-modified materials presented good antibacterial property. As a result, an effective and feasible method for the modification of polyethylene terephthalate was developed.