The multi-row pile quay wall is an innovative permanent structure comprising multiple piles, relieving slabs, flood control walls, and backfill sand. Although it additionally serves as a functional wharf, the research on multi-row pile quay walls remains insufficient. Considering the Changxing harbor Pool as a case study, this research develops a multi-row pile quay wall structure using the three-dimensional finite element software PLAXIS 3D. We investigated the effects of covered piles, pile row spacing, spacing between covered piles, and the stiffness of the front pile on the internal force and deformation of the structure. The findings indicated that the presence of the covered piles results in minimal overall displacement of the multi-row pile quay wall and reduces the bending moment in the front pile. Considering the site conditions and project costs, the sensitivity of different parameters to the retaining effect was evaluated in the order of the stiffness of the front pile > pile row spacing > spacing between the covered piles. Building on this, an optimized design scheme is proposed to reduce the bending moment in the front pile by 50% compared to the original scheme, thereby offering valuable insights for future engineering projects.