Isoquinoline (IQL), as a typical nitrogen-containing heterocyclic contaminant in coking wastewater, poses a serious threat to the aquatic environment and human health. Due to its chemical stability, traditional sewage treatment technology is not highly efficient in IQL removal. Advanced oxidation processes (AOPs) driven by ultraviolet radiation could be an effective treatment method, but it could generate toxic byproducts. In this work, the removal of IQL initiated by HO•, ClO•, Cl•, and SO4•- in UV/chlorine and UV/persulfate (PDS) process was comprehensively investigated, clarifying the degradation mechanism, reaction kinetics, and ecological toxicity. The findings indicate that the dominant oxidation mechanism of IQL by HO•, ClO•, and Cl• is radical adduct formation (RAF), while single electron transfer (SET) is the main reaction pathway of SO4•- with IQL. At 298 K and 1 atm, the order of rate constants for the reactions of IQL with active radicals is Cl• (6.23 × 1010 M-1 s-1) > SO4•- (8.81 × 109 M-1 s-1) > HO• (1.66 × 109 M-1 s-1) > ClO• (1.62 × 108 M-1 s-1). The acute and chronic toxicity of IQL and its degradation byproducts at three different trophic levels were evaluated using ECOSAR program. The byproducts produced by the oxidative degradation of IQL by HO• and SO4•- are mostly “not harmful”, and their toxicity shows a decreasing trend compared to that of IQL. The byproducts derived from the reaction of IQL with Cl• are all “toxic” or “harmful”, and the ranking of harm to three types of aquatic organisms is green algae > fish > daphnia. Hence, UV/PDS process could be more secure in pollutant disposal in wastewater. In actual water treatment process, merit attention should be paid to the potential hazards of the byproducts generated by various contaminants.