This paper measures the efficiency of ports in the Yangtze River Delta Region(YRDR) in 2008 and 2013 using port berth quantity, quay length, and human resources as input indicators, using cargo and container throughput as output indicators, and considering traditional(foreign trade dependence and industrialization level) and modern environmental factors(traffic line density, financial development level, and informatization level). To achieve such aim, this study constructs a multi-stage data envelopment analysis model(DEA) that identifies effective port decision-making units(DMUs) and generates a highly accurate conclusion by eliminating the interference from the exogenous environment and random errors. First, the external environment significantly affects port efficiency, with the traditional environmental factors showing huge fluctuations and the modern environmental factors producing great benefits. Second, the efficiency of ports in YRDR has increased from 2008 to 2013 primarily because of their pure technical efficiency. Third, the weighted standard deviation ellipse(SDE) analysis results reveal that the efficiency pattern of ports significantly deviates from their throughput pattern, while the center of SDE of port efficiency moves from the eastern coastal regions to the northwest regions. Based on these findings, this paper proposes spatial development strategies for YRDR, such as creating an unblocked environment where spatial elements can freely circulate, intensifying port-city joint development, implementing differentiated policies, and focusing on the spatial collaboration of port efficiency. This paper measures the efficiency of ports in the Yangtze River Delta Region (YRDR) in 2008 and 2013 using port berth quantity, quay length, and human resources as input indicators, using cargo and container throughput as output indicators, andially traditional (foreign trade dependence and industrialization level) and modern environmental factors (traffic line density, financial development level, and informatization level). To achieve such aim, this study constructs a multi-stage data envelopment analysis model (DEA) that identifies effective port decision-making units (DMUs) and generates a highly accurate conclusion by eliminating the interference from the exogenous environment and random errors. First, the external environment significantly affect port efficiency, with the traditional environmental factors showing huge fluctuations and the modern environmental factors producing great benefits. Second, the efficiency of ports in YRDR has increased from 2008 to 2013 primarily be cause of their pure technical efficiency. Third, the weighted standard deviation ellipse (SDE) analysis results reveal that the efficiency pattern of ports significantly deviates from their throughput pattern, while the center of SDE of port efficiency moves from the eastern coastal regions to the northwest regions. Based on these findings, this paper proposes spatial development strategies for YRDR, such as creating an unblocked environment where spatial elements can freely circulate, intensifying port-city joint development, implementing differentiated policies, and focusing on the spatial collaboration of port efficiency.