Mangroves acted as sinks of terrestrial pollutants, but the occurrence and contamination of rare earth elements (REEs) in urban mangroves lacked systematic evaluation. In rapidly developing Shenzhen, China, four typical urban mangroves were selected to determine the REEs in urban mangroves, including Baguang mangrove (BGM) and Futian mangrove (FTM) featured with ecological preserve and central business district, respectively; Xixiang mangrove (XXM) and Shajing mangrove (SJM) both featured with industry district. The mean concentrations of total REEs (TREEs) in sediment (0–25 cm depth, μg g⁻¹) were SJM (465.28) > FTM (411.25) > XXM (342.76) > BGM (118.63), with Ce to be the dominant REEs element. The depositions of REEs in urban mangroves were significantly affected by sediment sulfur accumulation and fine sediment, including silt and clay fractions. The main fractionation pattern of REEs in urban mangroves was the enrichment of light REEs (LREEs) and loss of heavy REEs (HREEs). Geo−accumulation index, modified degree of contamination, pollution load index, and potential ecological risk index showed the moderately contaminated level of REEs in FTM, followed by SJM, and XXM, with uncontaminated level in BGM. This study provided important information on REEs in urban mangroves for pollution prevention and remediation in the future.