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The importance of Structural Health Monitoring (SHM) is one of the keys to the sustainability of the structural system to be able to continue to provide services in accordance to its functions. The SHM process involves observation over the time to measure structural responses periodically. The aim of this study is to derive the governing equations to calculate the dynamic response of the structure including its natural and essential boundary conditions through the Hamilton Principle which involves kinetic and total potential energy of the system. Windmill structure as the object of this research is located in the middle of the sea. This offshore structure is idealized as a cantilever beam with lumped mass at the free end to represent the large fan installed there. Both waves and wind loads are considered in deriving the dynamics formulation. Deflection and external load functions inside the fourth order differential equation of the beam vibration are assumed to be known using the linear independent characteristics of polynomials. In order to establish the dynamics deflection response and the force acting on the structure, the strain data at different positions obtained from measurement of the structure are provided. Finally, matrix inverse formulation to estimate the actual force can be formed. By estimating the actual loads using this back-calculation, the structural response in various position at any time along the height of the system could be predict through forward analysis.