[Objective] To explore the effects of different concentrations of chlortetracycline on the characteristics of microbial communities involved in inorganic phosphorus (Pi) dissolution and organic phosphorus (Po) mineralization in the soil applied with organic fertilizer, focusing on soil P transformation and availability. [Methods] The purple soil collected from Tongnan District of Chongqing was used for a pot experiment with the addition of chicken manure as the organic fertilizer. Three chlortetracycline treatments (No-CTC, Low-CTC, and High-CTC) were designed with the addition levels of 0.0, 0.1, and 4.0 mg/kg, respectively. The soil samples were collected on days 7 (D7) and 30 (D30) after pepper ('Xinxiang 8') was planted. Real-time qPCR and Illumina MiSeq high-throughput sequencing were employed to analyze the community characteristics of the bacteria carrying the key genes (pqqC and phoD) of Pi dissolution and Po mineralization, respectively. Furthermore, the sequencing results and biologically based P (BBP) fractionation were employed to examine the effects of CTC addition on soil P transformation. [Results] High-CTC increased the content of Citrate-P and Enzyme-P by 8.2% and 44.0%, respectively, compared with No-CTC on D7. Low-CTC and High-CTC increased the content of Enzyme-P by 44.0% and 65.6%, respectively, compared with No-CTC on D30. The addition of CTC suppressed alkaline phosphatase (ALP) activity and affected the community structures of pqqC and phoD-harboring bacteria in the soil. The Mantel test results showed that Citrate-P was significantly associated with the dominant pqqC-carrying taxa Pseudomonas, Geodermatophilus, and Saccharothrix on D7. The dominant phoD-carrying taxa Bradyrhizobium, Ensifer, and Skermanella exhibited notable correlations with Enzyme-P on D7, and such correlations weakened over time. The average degree of the community network of the bacteria carrying pqqC increased in the Low-CTC treatment and decreased in the High-CTC treatment on D7. The average degree of this network decreased in High-CTC and Low-CTC treatments on D30. The average degree of the community network of the bacteria carrying phoD decreased with the increase in CTC addition on D7, while this trend was opposite on D30. [Conclusion] The addition of CTC significantly affected soil Enzyme-P by regulating the community structure of pqqC- and phoD-carrying bacteria as well as acid phosphatase (ACP) and ALP activities, thereby affecting the P forms and availability in the soil. This study contributes to a deeper understanding of alterations in microbial communities associated with P cycling in the soil-plant system contaminated by CTC. Moreover, it lays a scientific foundation for enhancing nutrient utilization efficiency in the soil applied with antibiotics.