The invention discloses a method of monitoring faults in sections for an intermittent control system and relates to a fault monitoring method. Firstly, a plurality of batches of collected intermittent process data are standardized in a way of expanding variables, and a data matrix on each sampling time is subjected to principal component analysis; secondly, a fuzzy C-means clustering is a fuzzy clustering analysis method which is suitable for soft partition and is generated through combining a fuzzy set theory and a k-means clustering; and thirdly, after segmentation is finished, an improved MPCA (Multiway Principal Component Analysis) model with a time varying principal element covariance on the basis of expanding variables is established on each subphase, then when on-line monitoring is carried out, which phase a new batch of data belongs to is judged, whether the data exceeds the fault monitoring control limit or not is calculated and judged, if so, a fault occurs, and the fault monitoring in sections ends. According to the invention, process multi-phase partition is more accurate, misinformation and missing report rates in monitoring are reduced, and the practical application and operability are strong.