According to the analysis of laser-pulse encoding modes, a method to decode laser-pulse series based on autocorrelation matrix statistic is put forward. The received laser-pulse series are used for constructing first order difference autocorrelation matrix and second order difference autocorrelation matrix. The elements of the two autocorrelation matrixes are counted in histogram mode. The laser-pulse series encoding mode can be classified by the characteristic of the two histograms, the time parameter of the pulse can be calculated out. The validity of the algorithm is tested by emulating experiment. Different modes of encoding laser-pulse are generated, and the missing probability and false probability are set, then the laser-pulse series are decoded by the algorithm. The emulating experiment shows that the algorithm has high precision, good real-time and anti-interference performance.