Pollution status and benthic ecological quality of the two types of ports were assessed based on heavy metals and macrofaunal assemblages. Macrofaunal abundance and biomass in the industrial port were significantly higher than those in the fishing port. The dominant species of the two ports were Echinocardium cordatum and Nephtys oligobranchia. Results of marine sediment quality assessment revealed more severe oil pollution in the fishing port than that in the industrial port. The AZTI marine biotic index (AMBI), multivariate AMBI, and Shannon-Wiener diversity index demonstrated that the benthic ecological quality of the two ports was moderate to good. The benthic ecological quality of the distant port sites was better than those of the nearby port sites. Heavy metal analysis indicated that mercury posed a serious threat to port sediment pollution. The dominant species and Pielou’s evenness index were significantly correlated with heavy metal pollution and were good biological indicators.