Assessing the sustainability development efficiency of port cities is an essential step toward improving their management. However, current research on this topic is limited, which makes it difficult for policymakers and urban planners to make informed decisions. To address this issue, we focused on 10 port cities in China as the subjects of our research. This was achieved using input indicators such as quay length, number of berths, labor population, and energy consumption, and output indicators such as cargo throughput, container throughput, smoke dust (DUS) emissions, sulfur dioxide (SO₂) emissions, the average annual concentration of respirable fine particulate matter (PM2.5), wastewater (WW) emissions, and GDP. The sustainability efficiency of 10 port cities is assessed over the period 2018-2021. This was achieved using the super-efficient SBM model and the Malmquist Index Model. We were able to accurately determine the levels of sustainability of the 10 port cities, and 7 were found efficient while 3 were found inefficient. The sustainability of the inefficient port cities is mainly affected by the number of berths, quay length, container throughput, DUS and SO₂ emissions, cargo throughput, water waste emissions, and GDP growth. Between 2018 and 2021, the annual mean total factor efficiency of Chinese port cities is less than 1, indicating a lagging situation that needs to be improved by optimizing port operations management and organization. The outcomes of our study can provide valuable insights for policymakers and stakeholders in port cities worldwide.