An inherent feature of batch processes is multiple operational phases. So many different phased-based monitoring methods had been proposed in order to monitor batch processes with multiple phases. The key of those methods is how to divide the phases of batch processes. At present, the most of the existing phase-division methods segment the batch process into several phases, where the same phase for difference batch run has equal duration. However, due to production conditions or other factors, the every phase's duration for different batch run is different. To solve this problem, a novel phase division method based on Fisher Discriminant Analysis (FDA) and Dissimilarity Index (DISSIM) is proposed in this paper. In DISSM-FDA algorithm, DISSIM is used to determine start and end points for each phase and rough division results are given. Then, the unequal phase division algorithm is advanced based on FDA that used to extract the phase characteristics. Application results to an industrial typical multi-phase streptomycin fermentation process show the effectiveness of the proposed method.