We applied the Hilbert differential contrast phase electron microscopy technique for the first time to mammalian cells, Ptk2 cells. Intracellular architectures such as the cytoskeletal network, membranous organelles, and mitochondria were observed without prior removal of cell membranes or extraction of soluble proteins. The attachment of mitochondria and membrane organelles with microtubules were observed. Microtubules were depolymerized by nocodazole treatment as expected. Thus, Hilbert differential contrast phase electron microscopy of vitrified cells is a nano-scale molecular imaging technique that opens up new vistas for exploring the supramolecular organization of the mammalian cell.