Effluents from wastewater treatment plants has been identified as a main point-source of antibiotics and antibiotic resistance genes in natural water environments. In this study, a typical municipal sewage treatment system in south China was taken as the research object to investigate the effects of each treatment unit on eight target antibiotics (sulfamethoxazole, sulfamethazine, tetracycline hydrochloride, oxytetracycline dihydrate, norfloxacin, ofloxacin, clarithromycin, roxithromycin), 17 antibiotic resistance genes (ARGs) and class 1 integron genes in the system using Accelerated Solvent Extraction-Solid phase extraction-Ultra high Performance Liquid Chromatography-Tandem mass spectrometry (ASE-SPE-UPLC-MS/MS) and real-time fluorescent quantitative PCR (qPCR) and the correlation between them. Seven antibiotics (mainly sulfonamides and tetracyclines, 4.19–141.97 ng·L−1) were detected in the influent, while only sulfamethoxazole, sulfamethazine, ofloxacin, and clarithromycin were detected in the effluent (3.11–16.61 ng·L−1). The tetracycline antibiotics in the wastewater treatment plant (WWTP) were transferred to the sludge phase by adsorption, in which tetracycline hydrochloride and oxytetracycline dihydrate were mostly removed in the aerobic and anaerobic stages, while sulfamethoxazole was mainly removed through biological transformation. Sul I was the most abundant resistance gene, but the WWTP had no obvious effect on its removal. Anaerobic treatment was found to play an important role in tetA, tetQ, and tetX removal. Moreover, correlation analysis revealed that the relative abundance of tetX was significantly correlated with clarithromycin (p = 0.039) and ofloxacin (p = 0.028), while that of tetQ was significantly correlated with sulfamethazine (p = 0.007) and sulfamethoxazole (p = 0.001), and that of tetC was significantly correlated with the class 1 integron gene (p = 0.014). Overall, the results presented herein provide a reference for improving the antibiotics and ARGs removal efficiency of WWTPs in south China.