The windmill towers are the tall structures which are used as supporting mechanism for mounting the nacelle and rotor of windmill. These tower structures are conventionally steel structures with monopole configuration. It may be possible that these towers are installed in area of high earthquake risk and they are subjected to natural disaster like earthquake during its life span. The conventional monopole towers are not useful for very tall windmill tower in seismically active regions owing to slender effect. To reduce damages in conventional monopole tower constructed in near filed seismic regions, the new hybrid structural system which is blending of monopole and lattice configuration is proposed in present research. The mass and stiffness of structure are important parameters to resist the seismic forces, therefore in present research, new structural configuration is proposed which gives more stiffness to structure. The 125 mt high conventional monopole windmill tower is modelled in the numerical simulation and appropriate model of hybrid tower is also modelled in FE software. Both monopole and hybrid towers are subjected to natural disaster like earthquake, considering different near field and far filed Seismic excitation. Detailed dynamic analysis of both towers was carried out and response of monopole and hybrid tower was compared for parameters like displacement in time domain, baes shear in time domain and response spectra of structure. From the results obtained using numerical investigation, it is concluded that the innovative hybrid structural system is more effective in tall windmill tower and can be used efficiently to resist the natural disasters like earthquake.