Microplastics (MPs), known to cause environmental pollution, is attracting a growing attention worldwide owing to their extensive existence and potential risks to biota. The marginal sea areas are suspected to be especially susceptible to MPs pollution. Unfortunately, data on MPs in the surface water and sediments ecosystems are still limited, particularly in the southern coastal areas of China. The study was successfully utilized to explore the distribution and characteristics of MPs below 5 mm collected from 14 sites in the seas around Shenzhen, a typical special economic zone of China. MPs were detected in both surface water and sediments with concentrations ranging from 3.8 to 7.8 items per liter and 2.6 × 103 to 10.0 × 103 items per kilogram, respectively. The highest abundance of MPs appeared in S5/S9 and S14 in surface water and sediments, respectively. Fiber and film with small particle size (<0.5 mm) were identified as typical and abundant MPs type among all samples. In addition, polyethylene (PE) was considered as dominant forms of MPs in surface water and sediment samples. Results from this study indicated a positive correlation with abundance of MPs and urbanization rate, which also showed an evident difference of MPs in different urban functional areas. Based on the types and quantity of detected MPs, we assessed the risk of MPs pollution in this study area, and the ecological risk category of MPs was at a high level. Importantly, our work might be employed as a potential information so as to better understand MPs pollution, source tracing and ecological risk assessment, which enhances the possibility of achieving effective control and supervision of MPs pollution in southern coastal aera of China.