Four carbon sources (including trehalose, glucose, acetic acid, and yeast extract) were used as the co-metabolic matrix of pentachlorophenol (PCP). The effect of the carbon sources on the process of acclimatization and degradation of PCP was investigated. The acclimatization rate of carbon sources with different substrates, the activities of microbial enzymes in the co-metabolism process, and the control of co-metabolism reaction conditions were evaluated. The kinetic model of co-metabolic degradation of PCP in micro aerated sequencing batch reactor (SBR) was established based on the Monod equation. The model was applied to fit the operating conditions of the micro aerated SBR process in this study. The experimental results showed that the type and concentration of metabolic matrix greatly influenced the degradation rate of PCP, and its trehalose, glucose, and acetic acid enhanced the degradation of PCP. In particular, the strengthening effect of trehalose was pronounced. When trehalose was used as a co-metabolic carbon source, the time required for PCP degradation to a predetermined degree was shortened to one-fifth of the original, PCP removal rate exceeded 95%. At the same time, yeast extract inhibited the biodegradation of PCP when it was used as an additional matrix carbon source. After the co-metabolism carbon source was added to the system, the proliferation rate of the microorganism was increased, and the key enzymes of PCP degradation were induced in the system. When the co-metabolic carbon source concentration was high, it accelerated active enzymes’ induction and maintained high activity; 2,3,5-triphenyltetrazolium chloride-electron transport system (TTC-ETS) activity reached about 7.6 mgTF/(gTSS·H), and 2-(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyl Tetrazolium chloride-electron transport system (INT-ETS) activity reached 63.5mgINTF/(gTSS·H). When the concentration of co-metabolism carbon source was extremely high, the co-degradation of toxic organic compounds was inhibited, leading to a decrease in the co-degradation rate. The kinetic model optimized the co-metabolism substrate. The degradation rate of PCP was increased by 54.9% by micro-aeration-co-metabolism. The kinetic model was used to fit the microaerobic reaction process of micro aeration SBR. The relevant result was in agreement with the experimental result by 97.6%.