Electrochemical advanced oxidation processes (EAOPs) have shown great potential for the treatment of shale gas produced water (SGPW). In this study, we investigated the transformation of dissolved organic matter (DOM) during EAOPs of SGPW and the formation of toxic halogenated by-products at various current densities, using fluorescence spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry. We found that the priority of DOM removal was terrestrial humic-like > microbial humic-like > protein-like substances. Non-Halogenated organic compounds (non-HOCs) and HOCs were predominantly CHO, and CHOCl/CHOBr compounds in EAOP-treated SGPW, respectively. As applied current density and treatment time increased, the production of oxyhalides increased, with chlorate > bromate > perchlorate. Meanwhile, most DOM was mineralized, resulting in residual products with higher modified aromaticity index (AImod) and nominal oxidation state of carbon (NOSC). The resistants had lower mass-to-charge ratio (m/z), AImod, NOSC, and double bond equivalent minus oxygen per carbon ((DBE-O)/C). The dominant reactions were the addition of tri-oxygen and deallyl. Bromine addition dominated the reactions of halogenating addition, while chlorine addition took second place. Furthermore, the acute toxicity of SGPW was positively correlated with inorganic halogenated by-products. This study contributes to the understanding and improvement of EAOPs for the treatment of SGPW.