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Scientific assessment of urban ecological security (ES) is an important prerequisite to realize regional sustainable development. Previous studies lack the consideration of quality and poor systematic correlation, which could not reflect the internal dynamic relationship. On the basis of considering the time lag, this study divided the research process into the natural operation stage and the management feedback stage based on the driving forces, pressures, state, impacts, responses, management (DPSIRM) framework model and DEA theory, so as to effectively overcome the above shortcomings. Finally, we analyzed the spatio-temporal characteristics and influencing factors of the ES level of 108 cities in the Yangtze River Economic Belt (YREB) during 2005–2019. The results showed that: (a) both two stages showed a slow and fluctuating upward trend in time series, and the level of urban ES in the management feedback stage was significantly higher than that in the natural operation stage; (b) with the passage of time, the spatial distribution of ES in the natural operation stage gradually developed towards the middle and downstream of the YREB, while the management feedback stage mainly evolved from the midstream to the edge area; (c) the level of urban ES presented a different degree of spatial agglomeration phenomenon, and showed an increasing trend over time; and (d) the key influencing factors gradually changed from pressure to response during 2005–2019. This research aims to provide an innovative perspective for the measurement of urban ES, and provide scientific reference for improving urban ecological sustainable development. [ABSTRACT FROM AUTHOR]