An investigation was conducted to characterize the trace element status of mangrove soils of Qi’ao Island in the Pearl River estuary. The results show that the spatial variation in the soil-borne trace elements in the investigated area was minor and most of the trace elements were at a level higher than those in other mangrove wetlands around the world, suggesting the mangrove soils of Qi’ao Island were heavily contaminated by trace elements transported from the Pearl River in the past two decades. Zn was closely related to Pb, Cu, Cd, and As, while some trace elements were not closely related to each other, indicating that they were derived from different sources. An integrated Nemerow pollution index of the surface soils at the 17 sampling locations ranged from 7.53 to 48.42, values which all fall within the highest pollution category. Among the 17 sampling locations, six locations had an ecological risk index (ERI) greater than 300, and 12 locations had an Ecological Risk Index (ERI) greater than 600, indicating that most of the investigated locations were at high or very high ecological risk. The findings obtained from this study have implications for understanding the terrestrial inputs of trace elements into part of the Pearl River estuary. This understanding can be used to guide the development of management strategies for controlling the discharges of trace elements from the catchment area and managing the aquatic ecosystems in the Pearl River Estuary.