The diagnosis of elution chromatographic patterns, being a vital step in chromatographic analysis, builds fundamental ingredient for later curve resolution or fitting. Many conventional multivariate resolution methods usually hold the hypothesis that the component, which appears first, will disappear first in the resolution of chromatographic systems. However, in real systems, such elution pattern is not always true. In this paper, a new method, named sectional moving window factor analysis (SMWFA), was proposed to diagnose the elution pattern of each chromatogram without any additional assumptions. The presented method was fast, friendly and helpful for automatic resolution of hyphenated chromatographic data. The performance of analyzed results in crude oil and traditional Chinese medicine (TCM) systems showed its efficiency of the proposed method.