This paper optimizes the scheme of side-by-side mooring operation for a special SWATH. Through numerical simulation and model tests, we analyze relative motions, mooring line tensions, and fender loads between the SWATH and single-body ship, aiming to guide the side-by-side mooring operation. The results show that the displacement difference of SWATH significantly affects the horizontal motion of the barge and the motion of SWATH itself. Changes in wave direction have a notable impact on the horizontal motion of both ships. Under the same relative motion, short mooring lines and fenders bear large loads. Therefore, it is recommended to select optimal wave directions (e.g., head seas) and loading states for operations. Beam seas (90°) pose the highest risk due to excessive fender compression. The research provides references for the design and optimization of side-by-side operations between SWATH and ships.