The recent advance on accelerator based X-ray and electron pulses have brought us novel tools to probe molecular process. In this talk, I would describe my recent research on this topic, including the ultrafast X-ray spectroscopy, Coulomb explosion momentum mapping, and quantum diffraction. Thanks to the ultrashort and ultrabright x-ray and electron pulses, it is possible for us to do quantum tomography, ghost diffraction and incoherent diffraction on molecules, which open up a new area of diffraction analyses.