To reveal the vertical distribution characteristics and potential ecological risk of nutrient elements and heavy metals in the sediment of a black and odorous urban river, taking the Nanhe River in Nanjing City as an example, sediment columnar samples (0 ~ 120 cm) from four sections were collected to analyze contents of total nitrogen (TN), total phosphorus (TP), organic matter (OM) and heavy metals (Cr, Ni, Cu, As, Cd, Hg, Pb, and Zn), and their potential ecological risk assessment and correlation analysis were studied. Results show that the nutrients and heavy metals in the sediment exhibited wide spatial differences, which is that the contents of TN, TP and OM in the sediments of northern section were significantly higher than those in the southern section. TN and TP increased with the depth and then decreased, with peaks at the depth of 40 ~ 80 cm. Contents of heavy metals in the southern and northern sections were higher, particularly the contents of Ni, Cd, and Pb in the sediments in the southern section and the contents of Cu, Hg, and Zn in the northern section reached more than twice of the middle section. Along the depth direction, except Hg and Zn, the content of heavy metals increased gradually with the depth within 60 cm. Potential ecological risk assessments showed that Hg and Cd in the sediments reached a very strong ecological hazard level, followed by Ni and Zn, while as showed little ecological hazard. Correlation analysis showed that Cu was significantly correlated with TP, TN, and OM, Ni and Cr were significantly positively correlated with Zn, and Cd, Pb, As, and Zn were significantly positively mutual-correlated. Heavy metals and nutrient elements in the sediment reached a high pollution level and showed a compound pollution trend.