This study used gas chromatograph-mass spectrometer (GC-MS) to determine three kinds of halogenated organic pollutants (HOPs) in the edible muscles of nine fish species in the Laibin section of the Hongshui River of Xijiang River in the Pearl River system. The results showed that the sum of organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs) in fish muscle was 8.94∼43.32 ng/g ww, 1.22∼4.09 ng/g ww, and ND∼0.13 ng/g ww, respectively. Evaluation indicators include analysis of the composition of homologous compounds, residues in different diets and habitats, and estimated daily intake (EDI) calculations. The analysis of the composition characteristics of homologous compounds showed that endrin was the most dominant in OCPs; hexachlorobenzene was the most dominant in PCBs; and BDE 154 was the most dominant PBDEs. Calculations of the levels of the HOPs in fish of different diets and habitats showed that OCPs and PCBs had the highest residues in carnivorous fish, and PBDEs had the highest residues in herbivorous fish. The residual OCPs, PCBs, and PBDEs in demersal fishes were the most. The estimated daily intake (EDI) results showed that daily fish consumption in the Laibin section of the Hongshui River would not cause HOPs health risks to the local residents. However, there is still a need for continuous monitoring of HOPs to reduce pollutant emissions and prevent pollution conditions from arising.