In this paper, we propose an algorithm to track multi-small targets in infrared image sequences in case of dissipation or creation of targets by using the background estimation filter, Kahnan filter and mean shift algorithm. We detect target candidates in a still image by subtracting an original image from an background estimation image, and we track multi-targets by using Kahnan filter and target selection. At last, we adjust specific position of targets by using mean shift algorithm In the experiments, we compare the performance of each background estimation filters, and verified that proposed algorithm exhibits better performance compared to classic methods.