The effects of rough sea surface on the long-range bottom reverberation in shallow seas are studied by the coupled mode reverberation theory. The scattering effect caused by irregular rough sea surface is described by couple coefficients. The decaying rules of long-range bottom reverberation level are simulated at different sea states, and the rough sea surface effect on the coherence of distant bottom reverberation is also discussed. It is indicated that irregular upper boundary has changed the propagation effect of the shallow water waveguide, and bottom reverberation, which is dominated among other kinds of reverberation in shallow water, is affected by the sea surface scattering as the increasing sea state. Compared with other literatures, the emphasis of this paper is to present the mechanism of rough sea surface scattering by describing the transfer of energy between different modes, and the details of energy transitions between different modes which are caused by sea surface scattering are presented for different sea states. With the increasing sea state, stronger mode coupling caused by surface scattering would affect the intensity and its space coherence of bottom reverberation obviously.