One high fidelity numerical method is extended to compute the unsteady aerodynamic loads when micro rotary wings suffer wind. The unsteady solutions are obtained by solving Navier-Stokes equations, where field velocity method is proposed to carry out the atmospheric perturbation. The convective terms are approximated by a high order WENO-Roe scheme, and time advance is performed by an implicit scheme of dual time stepping which can guarantee a degree of efficiency. Moving overset grids are used to facilitate the implement of rotational motion of rotary wings and relative movements between rotary wings, as well as the atmospheric perturbation. The results reveal that small atmospheric perturbation has an important impact on the flows of micro rotary wings under low Reynolds number. The response of thrust coefficient presents periodic fluctuation and its amplitude is proportional to that of wind disturbance, which provides the clue for active control research of rotary wing aircraft.