Design of a very large floating structure (VLFS) deployed near islands and reefs, different from those in the open sea, inevitably faces new technical challenges including numerical analysis methods. In this paper, a direct coupling analysis method (DCAM) has been established based on the Boussinesq equations and the three-dimensional hydroelasisity theory with Rankine source method to analyze the responses of a VLFS in shallow sea with complicated geographical environment. Model tests have been carried out to validate the DCAM. To further verify the numerical methods and investigate the performance of such a VLFS, a “Scientific Research and Demonstration Platform (SRDP)” was built and deployed in 2019 at the site about 1 000 m off an island with water depth around 40m in South China Sea. It is a simplified small model of a two-module semi-submersible-type VLFS. The numerical simulation of its responses on severe waves with focus on motions and connector forces is conduct by DCAM, and compared with the on-site measurements. Good agreement has been achieved. This approves the DCAM as a feasible tool for design and safety assessment of a VLFS deployed near islands and reefs.