It has already been reported that one-mass or lumped model of wind turbine system is insufficient to analyze the transient behaviour of wind turbine. For the sake of exact analysis of transient stability of wind turbines, it is needed to consider two-mass shaft system model. This model of drive train doesn't take into account the flexibility of blades. But it is usually used to calculate the electromagnetic torque reference allowing a Maximum Power Point Tracking (MPPT) strategy at low wind speed. In this paper we will compare the behavior of the controlled system, when the blades are supposed to be rigid and when their flexibility is taken into account using the Blade Element Momentum theory (BEM).