In order to improve the design effectiveness of large flat bottom ship with groove, a calculation method with combination of RANS equations and VOF two-phase-flow model was proposed for a large flat bottom ship with groove. The dynamic development of air layer in the groove was found. Based on the analysis of air layer fluctuations with different flow velocity, the difference of air layer fluctuation characteristics between three-dimensional and two-dimensional was explained and the fluctuation similar law of air layer was obtained. Numerical results show that: fluctuations of air layer appear in the groove and the wavelength of air layer increases with the increasing of velocity; the wavelength is equal to 0.64 times of the square of velocity; air layer presents phenomenon of coherent and reflection at the side walls of groove, so the wave height and the thickness of local air layer are changed; fluctuations of air layer is satisfied with Froude similarity.