The atmospheric turbulence is the main atmospheric disturbance affecting the flight. In this paper, the airplane of Citation 550 and the airplane of B747 are exampled to analyse the motion error affected by the atmospheric turbulence. Two simulation methods are used. The one is real-time simulation based on six degrees of freedom flight dynamics equations. The other is power spectrum density method based on the lineation small-perturbation equations. Compared with the data of flight tests, pros and cons of two methods have been studied. The results show that real-time simulation based on six degrees of freedom flight dynamics equations is more accurate and could be used for the simulation of large aircraft.