The port, industry and city are significantly related, and their integration degree reflects the coordinated evolution relationship among the three in the spiral development. Against the backdrop of deepening reforms in China's port management system, there is a growing need to scientifically assess the state of port-industry-city integration and analyze its underlying mechanisms. To address the issues of multidimensional indicator overlap and the difficulty in quantifying systemic synergy in existing research, this study constructs a coupling coordination degree model based on principal component analysis. Based on the panel data of 75 port cities in China from 2004 to 2023, the model applies principal component analysis to reduce the dimensionality of high-dimensional indicators across the port, industry, and city subsystems, thereby addressing multicollinearity issues among the indicators. Subsequently, a coupling coordination degree model is employed to quantify the level of synergy among the three subsystems, while the criteria importance through intercriteria correlation weighting method and panel entropy weight method are integrated for comprehensive weighting and robustness testing. The research shows that the overall integration level of Chinese port cities showed an upward trend during the study period, with its evolution exhibiting phased fluctuations influenced by the port management system. Significant disparities in integration were observed both across and within regions, with a maximum range of 4.65. Institutional changes in port management, path dependence in industrial development, and differences in regional institutional flexibility were identified as the core drivers of this spatial-temporal differentiation. Accordingly, policy recommendations such as establishing a cross-regional collaborative governance system and implementing differentiated industrial development strategies are proposed to advance the coordinated development of the port-industry-city system and provide a decision-making reference.