To explore the interaction mechanism between the alien species invasion via ballast water and coastal ecological environment security, this study employed the Pressure-State-Response (PSR) model as a framework to construct a comprehensive indicator system comprising 31 primary indicators for assessing the impact on the aquatic ecological security of shipping. The analytic hierarchy process (AHP) and entropy weight method were employed for combined weighting to dynamically evaluate the aquatic ecological security of shipping in China. This research represents the first systematic application of the PSR model and combined weighting method to the risk assessment of ballast water-mediated species invasion. It proposes a targeted management strategy of “identifying pressure-diagnosing state-optimizing response,” thereby supporting decision-making for the construction of a coastal ecological security barrier.