Coherent processing of multiple-input multiple-output (MIMO) radar with widely separated antennas has high resolution capability, but it also brings ambiguity in target localization. In view of the ambiguity problem, different from other signal processing sub-directions such as array configuration optimization or continuity of phase in space/time, this paper analyzes it from the information level, that is, the tracking method is adopted. First, by using the state equation and measurement equation, the echo data of multiple coherent processing intervals (CPI) are collected to improve the target localization accuracy as much as possible. Second, the non-coherent joint probability data association filter (JPDAF) is used to achieve stable tracking of spatial cross targets without ambiguity measurements. Third, based on the tracking results of the non-coherent JPDAF, the ambiguity of coherent measurement is resolved, that is, the coherent JPDAF is realized. By means of non-coherent and coherent alternating JPDAF (NCCAF) algorithms, high accuracy localization of multiple targets is achieved. Finally, numerical simulations are carried out to validate the effectiveness of the proposed NCCAF algorithm.