This paper presents a hydroelastic analysis of a hybrid-type VLFS in variable sea depth. The VLFS model is the prototype of a floating runway with dimension 3120m in length, 524m in width, 1.5m in draft for pontoon part and 11.5m in draft for semisubmersible part. A three dimensional Finite Element model using beams and quadrilateral plate elements are used in the hydroelastic analysis in order to obtain an accurate approximation. An equivalent plate model having the same eigenfrequencies and eigenmodes in air is also used in the analysis. The results using the 3D model and the plate model have been compared and their agreement is satisfying. In order to examine the variable sea depth at the expected site, the hydroelastic analysis is carried out for a flat bottom, a constant slope, and a variable sea depth case. The effect of variable sea depth is found to be significant.