The paper presents a method of dynamic analysis of the three dimensional beam structure containing rigid bodies and mass particles, partialy immersed in water. The governing equation is introduced into a stiffness matrix form by combining the solutions of four kinds of partial differential equations on vibration of beam, that is, those of two directions of bending, torsion and thrust. The orthogonallity of the general mode function composed of the four kinds of shape functions containing rigid bodies and mass particles is proved, in order to analyse the dynamic response of the structure by using the mode method. Assuming a fixed offshore structure as a structure constructed by a flat rigid deck with four legs, the theoretical results of the eigenvalues and dynamic stress distributions fairly agree with experimental ones.