A new differential image motion monitor (DIMM) system for measuring atmospheric coherence length which can track motion target is developed. The system uses a new algorithm which is composed of genetic algorithm and iterative centroid algorithm to process differential image and calculate the offset of the target and the covariance of the angle-of-arrival fluctuation in realtime. So, it can track motion targets and measure the atmospheric coherence length. In experiment, we use a halogen lamp tied in a stratosphere balloon at the altitude of 35 km as the lamp-house to measure the atmospheric coherence length along slant propagation path. Simultaneously, we put another instrument 5 m away from the new system which selects the solar limb as the lamp-house to measure the total layer atmospheric coherence length. The result indicates a linear correlation between the two groups of data. At last, we analyze and discuss the feasibility of a method which can use laser guide star to measure the total layer atmospheric coherence length.