Abstract: The quadrotor controller output is generally affected by wind disturbances which causes the unmanned aerial vehicle (UAV) lift coefficient to fluctuate violently, which reduces the controllability and stability of the quadrotor control. To solve this problem, we design a linear quadratic regulator (LQR) method combined with a compensation based on aerodynamic parameter estimation. First, we simplify and linearize the dynamic model of the quadrotor to design the position and attitude controller based on the optimal linear quadratic control theory. Next, we estimate the aerodynamic parameter online using Kalman filter and then compensate the speed of the rotors to improve the control of UAV altitude and yaw by the calculation of the coefficients' scale factor. Finally, several simulation experiments are done to validate the proposed method. The experimental results show that the proposed method outperforms the conventional methods in aerodynamic estimation and compensation, and thus yields a better control of UAV altitude and yaw.