Microplastics (MPs) present in non-negligible amounts in urban environments, where urban rivers serve as important transport channels for MPs. However, the footprint of MPs in urban rivers under the influence of natural and anthropogenic factors is poorly understood. This study investigated the MPs organization, stability and pollution risk before and after rainfall in the Qing River, Beijing. Rainfall potentially diluted the MPs abundance, attributed to opening of barrages and increase of flow velocity. The proportion of small-sized MPs (SMPs, 48–300 μm) decreased slightly, whereas that of normal-sized MPs (NMPs, 300–1000 μm) and large-sized MPs (LMPs, > 1000 μm) increased. However, SMPs dominantly presented in the Qing River before and after rainfall. Polyethylene terephthalate (PET), polypropylene (PP), polyethylene (PE), and polystyrene (PS) were main polymers observed in the Qing River. The proportions of PET and PS decreased, while PP and PE increased after rainfall. The main types of MPs introduced by stormwater were PP and PE. The elevated MP diversity integrated index after rain suggested that rainfall enriched the local sources of MPs. Rainfall reduced the stability and fragmentation of MPs owing to the introduction of large debris. NMPs and LMPs were susceptible to further fragmentation and downsizing, implying that MPs abundance in the Qing River tended to rise and SMPs might enriched. In addition, alteration of MPs fragmentation and stability reflected that the likely input source was wastewater treatment plant and atmospheric deposition before rainfall, whereas soil and road dust were possible sources after rainfall. The pollution risk assessment defined the MPs pollution risk of Qing River as low level and decreased after rainfall. This study demonstrated that rainfall substantially influences MPs organization in urban river and provided empirical support for MPs environmental behavior under influence of natural and anthropogenic factors.