The invention discloses a nanometer CT three-dimensional imaging method using three quantitative imaging mechanisms. The method comprises taking a valley macrophotograph, an upslope macrophotograph, apeak macrophotograph and a downslope macrophotograph of a sample at different angles on the image plane of an X-ray differential phase contrast microscope according to an angle signal response imaging mechanism, rebuilding a two-dimensional absorption contrast image, a two-dimensional refraction contrast image and a two-dimensional scattering contrast image of the sample at different angles on the object plane of the X-ray differential phase contrast microscope according to three quantitative imaging mechanisms, and rebuilding a linear absorption coefficient three-dimensional image, a linearscattering coefficient three-dimensional image, a refractive index real attenuation rate three-dimensional image and a refractive index real attenuation rate derivative three-dimensional image of thesample according to inverse Radon conversion. The method can realize three-dimensional imaging of whole cells with diameters of 5 micrometers or more and has the nanometer scale resolution rate.