The Ma’anshan section of the lower Yangtze River features a complex multi-anabranching system, where the river divides into several branches around mid-channel sandbars, with distinct point bars alternately developing along both banks. Within this morphologically active system, Zhengpu Harbor suffered severe operational disruptions by accelerated siltation at its approach channel, primarily due to its vulnerable location downstream of the expanding Niutun River point-bar on the left bank. To systematically diagnose the mechanisms of siltation, this study integrates multi-method investigations: decadal-scale morphodynamic analysis using long-term bathymetric surveys, numerical modeling to quantify engineering impacts on flow dynamics, and multiple linear regression analysis for the contributions of key influencing factors. The result identifies three primary drivers of siltation, collectively responsible for 70% of the sediment accumulation, including the rightward shift of the thalweg in the Ma’anshan left branch, reduced flow diversion of the left Branch of Central bar, and the expansion of the Niutun River point bar. River engineering structures, such as bridges, contribute approximately 12%, while changes in upstream flow-sediment supply account for approximately 18%. To mitigate siltation at Zhengpu Harbor’s approach channel, this study proposes targeted engineering interventions to enhance local hydrodynamic conditions. The spur dikes were designed to enhance the morphological stabilization of the Central bar head to regulate flow distribution. A diversion channel could also be excavated at the tail of the Niutun River shoal, and emergency dredging was recommended at the harbor front. Numerical modeling indicates that these measures will increase flow velocity by over 0.1 m/s at the harbor front, mitigating the siltation situation. The study concludes that the proposed engineering measures can reduce annual siltation by approximately 30% under normal-year hydrological conditions, demonstrating their feasibility in mitigating siltation trends in multi-anabranching river systems. This research provides a reference for addressing siltation issues in harbors within complex anabranching river systems.