A method of beam focusing control based on the spatial light modulation is proposed. In order to realize the rapid and precise adjustment on the axial and transverse deviations of the beam focusing, the liquid crystal spatial light modulator is adopted to produce the dynamic phase structure of binary Fresnel lens. An area array detector is used to detect the size and position of the light spot. And combining the feedback control mechanism, the automatic calibration and stability control on the beam focus point of three-dimensional position can be realized. In the adjustment process of this method, there is no coupling among different deviations, and the transverse deviation adjustments are insensitive to the propagation distance. Furthermore, the real-time feedback control system of beam focusing based on this method is introduced. The experiment results show that the axial calibration of the beam focal spot can converge precisely and rapidly. The transverse deviation calibration can converge with single step in the case of short focal length. In the case of long focal length, the combination of proportion-integration-differentiation algorithm is need to adjust. The convergence with single step can be also realized if an experiential correction on the adjustment errors based on the data fitting are corrected experimentally.