In chlorophenol wastewater treatment, adding easily degradable carbon sources, such as methanol, ethanol, sodium acetate, and sodium propionate, significantly improves the chlorophenol removal efficiency. This study systematically compares these conventional carbon sources in different sequencing batch reactors to understand their specific effects on both 2,4,6-trichlorophenol (2,4,6-TCP) degradation efficiency and microbial abundance. In a 35-day experiment, as a carbon source, ethanol exhibited a lower 2,4,6-TCP degradation concentration (77.56 mg/L) than those of methanol, sodium acetate, and sodium propionate, which achieved higher degradation concentrations: 123.89 mg/L, 170.96 mg/L, and 151.79 mg/L, respectively. As a carbon source, sodium acetate enhanced extracellular polymeric substance production (200.80 mg/g·VSS) by microorganisms, providing protection against the toxicity of chlorophenol and resulting in a higher 2,4,6-TCP removal concentration. Metagenomics identified crucial metabolic genes, including PcpA, chqB, Mal-r, pcaI, pcaF, and fadA. The abundance of genera containing the chqB gene correlated positively with the metabolic capacity for 2,4,6-TCP. Moreover, small molecular carbon sources such as methanol, sodium acetate, and sodium propionate promoted the enrichment of genera with functional genes.