EasyLaser is component-based laser system simulation software. Beam control system simulation is a main part of EasyLaser, which can be used for systems with multi-optical paths, multi-wavelength beams, and multi-controllers. A new numerical method about general kinematics separation is proposed for beam control system simulation. It provides axis rotation conversion relationships due to orientation data of apparatus of system, such as gimal, sensor and optical mirror. It gives their coupling and uncoupling matrixes in kinematics and controller model. The matrixes could change every iterative time automatically during the dynamic tracking process. The main advantage of the method is more suitable to solve the problems that the gimbal movement and geometry optical transmission are considered simultaneously. By using the method, sensor images and undershoot data are updated automatically. And further the kinematic driver or controller signals are separated automatically. Therefore the tracking and beam control can be designed without consideration of the system kinematical composition. Then the beam control system simulation has the virtues of generality, flexibility, and usability. No matter what kinds of gimbal and optical path, designer needs only to consider tracking and beam control aspects. In addition, a union beam control example for atmosphere transmission correction is given. It includes tracking tilt mirror and adaptive optics system. Simulation results show that the low-frequency fluctuation is restrained effectively and the high-frequency fluctuation is corrected obviously.