Municipal wastewater treatment plants (WWTPs) are considered to be major contributors of microplastics to the aquatic environment. Detailed research in China, which is relevant to the local situation, remains in the initial stage. Herein, the microplastic abundance, morphology, and removal efficiency of two WWTPs (C and P) equipped with tertiary treatment processes in different districts of Nanjing, an important city in the Yangtze River Basin, were investigated. The influence of technology, operational parameters, daily capacity, and sewage source and its proportion were discussed. Observations by optical microscope and FT-IR analysis and systematic calculation revealed that the microplastics have four shapes, including fragments, granules, film, and fibers, with various sizes and proportions, which were dependent on wastewater source. The total removal rates of 97.67% and 98.46% for WWTP C and WWTP P, respectively, indicated their highly efficient reduction of microplastics. Treatment technology had a considerable influence on the removal rate, especially the secondary and tertiary processes. However, a large number of microplastics from WWTPs were still released into the environmental waters due to the huge daily capacity. Sewage source determined the concentration, morphology feature, and chemical composition of microplastics to a certain extent. Compared with industrial wastewater, domestic wastewater possibly contained smaller microplastics of polyethylene and polypropylene with lower abundance. Furthermore, additional attention was provided on the flocculation process, drainage system, and treatment efficiency of microplastics with different shapes. This work is expected to provide some technical supports to guide the operation and management of WWTPs.