<p>In recent decades, Laizhou Bay has experienced significant habitat degradation, severe land-based pollution, and a progressive increase in the density of shellfish aquaculture. The potential impacts of these aquaculture activities on the ecological carrying capacity of the key commercial species, the swimming crab (<i>Portunus trituberculatus</i>), and the broader Laizhou Bay ecosystem remain unclear. This study developed a 3-year (2021–2023) Ecopath model using 2022 aquaculture data to estimate <i>P. trituberculatus</i>’s ecological carrying capacity and compare scenarios with and without aquaculture. Results show that including aquaculture significantly increased total system throughput but decreased net ecosystem production. Over the 3 years, it also reduced the average total primary production to total respiration (TPP/TR), total primary production to biomass (TPP/B) ratios, connectance index (CI), and system omnivory index (SOI), suggesting that intensive aquaculture may reduce ecosystem stability. When considering aquaculture, the ecological carrying capacity for <i>P. trituberculatus</i> in 2022 rose from 0.5468 to 0.5666 t·km⁻², indicating moderate shellfish aquaculture can positively affect its stock enhancement. However, based on various characteristic indicators of Laizhou Bay, shellfish aquaculture accelerates ecosystem destabilization. In the future, it is crucial to maintain moderate shellfish densities, implement multi-species polyculture, and optimize spatial planning through integrated multi-level aquaculture systems. Only through multi-tiered integrated aquaculture systems can we achieve comprehensive utilization of seawater nutrients and spatial resources in Laizhou Bay. This study represents the first integration of aquaculture into a Laizhou Bay ecosystem model, offering a scientific foundation for sustainable fisheries management and enhancement strategies.</p>