In order to improve the performance of space-based missile warning system in tracking multi-target, the latitude-zone scan mode and target-group track mode were proposed for the scanner and tracker respectively. Based on these modes, the scan sensor and track sensor management algorithms were proposed. For the multi-model sensors, their working mode, the scanning frequency, the measurement error and the field-of-view differ from each other, an observation tracking Cramer-Rao formula was derived. Finally, a multi-model senor management algorithm based on the above methods was proposed. Results show that the proposed algorithm has a higher tracking accuracy for multi-target than the system in traditional working mode. 