Histopathology examinations of H&E stained biopsied tissues is the golden standard for colonic diseases (e.g., polyps, adenoma, and adenocarcinoma) diagnosis. However, staining effect of sample and doctor's expertise degree may greatly influence the diagnosis results. The information provided by the H&E stained sample is also limited to the morphological and PH information and no quantative information is available. In this paper, we report the development of a unique multimodal nonlinear optical microscopy (i.e., hyperspectral stimulated Raman scattering (hsSRS), second-harmonic generation (SHG), third-harmonic generation (THG), two-photon excitation fluorescence (TPEF)) platform for the diagnosis and characterization of colonic diseases. HsSRS in both fingerprint (800–1800 cm-1) and high-wavenumber (2800–3600 cm-1) regions allows us to discriminate different constituents with tiny difference in the Raman spectra. The increase of proteins and reduction of lipids could be observed with the progress of colonic cancer. SHG shows the distribution of collagen, which is found to aggregate for adenocarcinoma. TPEF provides the cell morphological and can reflect the damage inside glands caused by the diseases. THG shows the increase of optical heterogeneity related to cancer process. This work shows that the integrated hsSRS and TPEF/SHG/THG imaging technique can be an effective method for digital pathology of colonic diseases at the molecular and sub-cellular levels.