The identification of the sequence of seal stamps and ink has always been a hot and difficult issue in the research and practice of forensic document examination, which could prove the authenticity of the documents and infer whether the documents are consistent with the facts of the case, thus providing a legal basis for the judicial department to investigate and judge the case. The common identification methods include optical microscopes, fluorescence, document inspection, and computer software-assisted methods. The identification conclusion is easily influenced by subjective experience and is questioned due to its lack of objectivity. In this study, based on the preparation of 54 handwriting samples of 3 types of signature pens and 9 types of seal stamp combinations, 18 printed samples of laser printed, and 9 types of seal stamp combinations, the samples were tested by Confocal Microscope Raman Spectrometer. The optimal condition was obtained from the handwriting samples (10# Pilotg-1) and seal stamps (1# Print show). The 72 prepared samples were placed in a dark storage box for one year. Under this optimal condition, the Raman spectrum of four measuring sites in the sample, followed by ink before seal stamps, seal stamps before ink, seal stamps, and ink, were measured, and each sample was tested three times. The experimental results were unaffected by storage environment or paper background factors. Whether handwriting or printed samples, the intersection of ink before seal stamps displayed some of the characteristics of the seal stamps. At the same time, the intersection of seal stamps before ink displayed some of the characteristics of the ink. The Raman spectra of the intersection showed most of the Raman shifts of the corresponding seal stamps or ink on the upper layers, consistent with the observation of μ View under a 20× objective lens. Raman shift of the sample was compared to identify the crossing sequence of seal stamps and ink of handwriting/printed. The results show that the novel method is convenient, quick, non-destructive, highly sensitive, and accurate and has practical guiding significance for identifying the crossing sequence of seal stamps and ink.