Mangroves bear enormous ecosystem value, while the ecosystems are facing increasing environmental pressures. In this study, 73 samples of soil sediments in mangroves, paddy fields, grasslands, forests, and shrimp ponds were collected from Shankou Mangrove National Nature Reserve (SKMNNR), Guangxi Zhuang Autonomous Region, China. The pollution status and ecological risks of heavy metal elements of Cr, Ni, Cu, Zn, As, Cd, Pb, V, and Co were determined using the enrichment factor (EF), geoaccumulaton index (I_geo), and potential ecological risk index (PERI). The average concentration is shown to be substantially lower than the background value. In general, the I_geo values indicated that the pollution conditions of different land use types in SKMNNR are relatively minor. Most of the PERI values were at the moderate level. This study demonstrates that the current status of sediment quality in SKMNNR is relatively good, and the pollution level is relatively low. Large-scale coastal aquaculture development and industrial expansion should not no longer be permitted there.