In this paper, a three dimensional soil-structure interaction (SSI) is numerically simulated using finite element method in order to analyse the foundation moments in annular raft of tall slender chimney structures incorporating the effect of openings in the structure and the effect of soil flexibility, when the structure-soil system is subjected to El Centro (1940) ground motion in time domain. The transient dynamic analysis is carried out using LS-DYNA software. The linear ground response analysis program ProShake has been adopted for obtaining the ground level excitation for different soil conditions, given the rock level excitation. The radial and tangential bending moments of annular raft foundation obtained from this SSI analysis have been compared with those obtained from conventional method according to the Indian standard code of practice, IS 11089:1984. It is observed that tangential and radial moments increase with the increase in flexibility of soil. The analysis results show that the natural frequency of chimney decreases with increase in supporting soil flexibility. Structural responses increase when the openings in the structure are also considered. The purpose of this paper is to propose the need for an accurate evaluation of the soilstructure interaction forces which govern the structural response.