Present study aims to investigate draft effects on hydro-elastic response of pontoon type VLFS(Very Large Floating Structure). A three dimensional higher-order boundary element method(HOBEM: Hong et al;1999, Choi, Hong and Choi; 2001) is extended to analyze elastic response of structures. Intensive numerical calculations were carried out for box type structure to investigate the draft effect on hydrodynamic forces on pontoon type VLFS. Main attention was paid to wave run-up along the waterline for various cases of draft scantling. It is found that the draft effects on the hydro-elastic response of pontoon type VLFS are important especially in short wave range and shallow water region.