Inaccurate substage division problems often emerge when multiway principal component analysis is applied in fault monitoring of multistage batch processes. A new two-step stage division method based on support vector data description (SVDD) is proposed in order to avoid the hard-division and misclassification problems. The loading matrices of the MPCA model are modified using the idea of combining the mechanism knowledge with field data in the rough division step. The model differences are increased by introducing the sampling time to loading matrices, which can avoid division mistakes caused by the fault data. Detailed stage separation is realized here based on the SVDD hypersphere distance to divide the process strictly into steady or transition stages. Then a soft-transition sub-PCA model is given based on the hypersphere distance. The method is applied to monitoring a penicillin fermentation process online. Simulation results show that the proposed method can describe transition stage information in more detail. It can detect the fault earlier and avoid the false alarm compared with traditional sub-PCA monitoring.