The rapid development in coastal areas leads to the increasing discharge of pollutants, which have posed certain threats to the coastal ecological environment. Among them, heavy metal is one of the main pollutants. In this paper, the enrichment coefficient method and potential ecological risk index method were used to assess the pollution ecological risk of heavy metal elements (V, Cr, Mn, Ni, Zn, Sr, Pb) from sediment cores in Haizhou bay. Meanwhile, multivariate analysis methods (correlation analysis and factor analysis), the absolute factor analysis-multiple linear regression (APCS-MLR) receptor model and positive matrix factorization (PMF) analysis were employed to qualitatively and quantitatively reveal the sources of heavy metals. The results showed that the concentration of heavy metals from sediment cores in Haizhou bay was generally higher than the background value, and it has little change before 1980, but has an upward trend after 1980, which was related to the rapid development of industrial economy in Lianyungang after 1980. The heavy metals from sediment cores in Haizhou bay belong to mild to moderate enrichment level and mild potential ecological risk level. Multivariate analysis showed that V, Mn, Zn and Sr mainly came from the mixture of agricultural pollution and natural sources. Cr and Ni were mainly controlled by industrial sources. Pb was dominated by traffic sources. The analysis results of APCS-MLR and PMF models were basically consistent with the multivariate analysis results. APCS-MLR and PMF model results showed that the contribution rates of agricultural and natural sources, industrial sources and traffic sources to heavy metal pollution were 39.81% and 45.75%, 48.49% and 35.08%, 11.67% and 19.17%, respectively. The results can provide an important basis for the prevention and control of heavy metal pollution in Haizhou bay.