This study aims to address organic micropollutants in secondary effluents from municipal wastewater treatment plants (WWTPs) by first identification of micropollutants in different treatment units, and second by evaluating an advanced treatment process for removals of micropollutants. In secondary effluents, 28 types of pharmaceutical and personal care products (PPCPs), 5 types of endocrine disrupting chemicals (EDCs) and 3 types of odorous compounds are detected with total concentrations of 513 ± 57.8 ng/L, 991 ± 36.5 ng/L, 553 ± 48.3 ng/L, respectively. An integrated process consisting of in-situ ozonation, ceramic membrane filtration (CMF) and biological active carbon (BAC) filtration is investigated in a pilot scale (1000 m3/d) for removal of micropollutants in secondary effluents. The total removal efficiencies of PPCPs, EDCs and odorous compounds are 98.5%, 95.4%, and 91.1%, respectively. Removal mechanisms of emerging organic contaminants (EOCs) and odorous compounds are discussed based on their physicochemical properties. The remarkable removal efficiencies of micropollutants by the pilot system is attributed to synergistic effects of combining ozonation, ceramic membrane filtration and BAC filtration. This study provides a cost-effective and robust technology with the capability of treating secondary effluents for reuse applications.