A reconstruction method for a pore structure of a core with micro-CT (Computed Tomography) is provided. With utilizing a FIB-SEM (Focused Ion Beam-Scanning Electron Microscope) experiment, an actual porosity corresponding to a grey level in micro-CT results is obtained, so as to establish a relationship between the grey level of a micro-CT image and the porosity. Thereafter, according to the above relationship, a certain porosity is assigned to each pixel in the micro-CT image, so as to establish a soft segmentation method of the pore structure. The reconstruction method provided by the present invention discloses a soft segmentation method for digital reconstruction of the pore structure of the core combined with FIB-SEM data and micro-CT data, and establishes a fractional digital pore structure model of the core, which further improves a matching degree between the digital pore structure model of the core and an actual core.