In order to achieve the real-time calculating about the flight trajectories of the multiple targets and guiding the equipment to track the targets, a real-time multi-target intersection method was proposed. Such method is based on the characteristic of target movement and the inherent characteristic of optic-electronic theodolite tracking measurement. This algorithm can achieve the goals of sorting homologous measurement data and eliminating the false target trajectory, and finally get the true target trajectory. The algorithm is applied to the optic-electronic theodolite measuring system which is under the condition of target N≤3 and communication cycle being 50ms. The experiment results show that the method can guide the measuring equipment to track accurately, stably and in real time.