The antibiotic erythromycin is an emerging pollutant frequently detected in aquatic environments. Microbial degradation is a crucial approach for eliminating erythromycin contamination. However, only a few efficient erythromycin-degrading fungi have been isolated, and the molecular mechanisms of erythromycin degradation, as well as their application potential, remain poorly understood. In this study, a novel erythromycin-degrading fungus, Aspergillus terreus RJJ-62 was isolated from a contaminated sample. Moreover, a fungal immobilization system was developed using strain RJJ-62, charcoal, polyvinyl alcohol and sodium alginate to enhance erythromycin degradation capacity. Strain RJJ-62 degraded 47.66% of 100 mg/L erythromycin within 120 h, while the immobilized RJJ-62 enhanced the removal efficiency by 25.79%. Furthermore, four key intermediates of erythromycin were identified by HPLC-MS/MS, and a new catabolism pathway of erythromycin degradation was unveiled, which erythromycin was degraded to simple products mainly by dehydration, desugar and ester bond hydrolysis reactions during the metabolic process. The biotoxicity analysis of the intermediate products confirmed that this approach was effective in detoxifying erythromycin in aquatic environments. Immobilized RJJ-62 also exhibited superior performance in complex wastewater, degrading 100% of 10 mg/L and 66.46% of 50 mg/L erythromycin within 7 days, respectively. Therefore, this study offers a feasible method for removing erythromycin in water environment and also strengthened our understanding on the erythromycin degradation process of fungi.