An integrated system for in vivo multi-spectral imaging (MSI) and Raman spectroscopy was developed to understand the external morphology and internal molecular information of biological tissues. The achieved MSI images were reconstructed by eighteen separated images from 400 nm to 760 nm, whose illumination bands were selected with six tri-channel band filters. Based on the spectral analysis algorithms, the spatial distribution patterns of blood volume, blood oxygen content and tissue scatterer volume fraction were visualized. In vivo Raman spectral measurements were executed by inserting specially designed optical probe into instrumental channel of endoscope. By this way, the molecular composition at selected sampling points could be identified with its fingerprint spectral information under the guidance of molecular imaging modality. Therefore, both structural and compositional features of intestinal membrane could be addressed without labeling and continuously. The achieved results testified that our presented methodology reveals insights not easily extracted from either MSI or Raman spectroscopy individually, which brings the enrichment of biological and chemical meanings for future in vivo studies.