Malachite green isothiocyanate(MGITC)is a Raman probe molecule that was applied to cells detection, tissue composition detection and cells stain imaging. In the present work, MGITC molecular structure was optimized by density functional theory(DFT) calculation. MGITC molecular Raman spectra and infrared spectra were calculated with Hartree-Fork theory and MP2 theory based on STO-3G level, then two theoretical Raman spectra were carefully compared with experimental spectra, and good agreements were obtained between the theoretical and experimental results. MGITC structure parameters were given also in the paper including bond lengths and bond angles etc. Vibrational modes were assigned to all bands in the range between 550 and 4 200 cm-1. This work will facilitate the application of MGITC Raman probe for biology.