With the rapid development of the South Korean economy, human activities have extensively affected Korea’s coastal environment. A precise ecological quality assessment remains paramount despite the relatively lower impact of human activities on the East Sea compared to the West and South Seas of South Korea. Accurate ecological quality assessments can provide valuable marine environmental protection and management references. In our study, we employed seven indices based on heavy metals and macrobenthos to comprehensively assess ecological quality. Our results indicated the final ecological quality in the central East Sea of South Korea was acceptable at most stations; however, the ecological quality in winter marginally falls short compared to that in spring. The concentration of heavy metals emerges as a significant determinant of the final ecological quality, underscoring the need for subsequent studies to investigate the origins of heavy metals in the central East Sea of South Korea and the influence of anthropogenic activities on heavy metal concentrations. Furthermore, employing a single biotic index proves challenging for accurately assessing ecological quality in the East Sea of South Korea.