For the supporting engineering of deep foundation pits in navigation locks, double-row piles with greater flexural rigidity are often used. Due to factors such as narrow construction areas, the double-row pile supporting structure in the expansion and renovation of navigation locks also needs to be combined with navigation requirements to form a permanent composite structure. The relevant codes do not specify the calculation method for the pile-raft combined supporting structure. For this new type of structure, different calculation methods yield significantly different results. To systematically study the deformation and internal force distribution characteristics of this structure under different calculation models, this paper compares the results of design based on reference codes with those calculated using solid models. By combining the field monitoring results of engineering examples and comparing them with the calculation results of solid models, the paper also proposes possible adverse conditions for the supporting of waterfront foundation pits. The results show that when designing according to relevant codes, the upper retaining wall undergoes linear displacement, and the bending moment and shear force of the rear piles are greater than those of the front piles. However, in the solid calculation model, the upper retaining wall undergoes translational displacement. Due to the main soil pressure difference caused by foundation pit excavation, the front piles experience greater bending moments and shear forces than the rear piles. The actual monitored displacement values in the project are greater than the model calculation results, suggesting that sufficient safety margins should be provided for the application of the pile-retaining wall composite structure in waterfront foundation pits. The above results can provide a reference for relevant codes regarding the calculation models of new structures and offer insights for similar supporting engineering projects in navigation locks.