An underground coherence function considering water-covered effect and suitable for simulating the seismic motions of media-transition V-shaped canyon is derived in this paper. The variation law and physical meaning are further investigated and summarized in detail. The underground PSD matrix is constructed by combining the derived coherence function， the transfer function and the obtained theoretical solution of scattering in media-transition V-shaped canyon with partly filled water. Subsequently， the multi-support underground seismic motions are generated by decomposing the underground PSD matrix， and the reliability and rationality is further verified. The effects of the proposed coherence function and the depth of water on the seismic motions and the responses of a continuous rigid frame bridge are compared and analyzed. Results show that： The coherence due to water effect is obviously enhanced. Moreover， the amplitude of seismic motions in the water-covered areas is reduced because the part of energy from P waves is transferred to the water. The amplitudes of ground motions and structural seismic responses correlate negatively with the depth of overlying water. In other words， the effect of water decreases with the increasing distance from water areas. The work in this paper is valuable for the simulation of multi-support seismic motions and dynamic analysis of those long-span structures located at the media-transition V-shaped canyon with partly filled water.