This paper presents mode indices as a function of time after proton-exchanged waveguides formed by immersing x-cut LiNbO3 into benzoic acid melts for certain period of time.The measured data show that there are instabilities in PE waveguieds. The instabilities depend on fabrication parameters and operation temperature.The reasons to cause the instabilities and measures to overcome them are proposed.The measurements of infrared absorption and secondary ion mass spectrometry（SIMS）identify that our views on PE waveguides instabilities are reasonable.