To quantitatively evaluate the pore size distributions (PSD) contributed by various components (PSDCVC) in over-mature shale samples, the Upper Ordovician Wufeng Shale from Southeast Chongqing was taken as an example. The PSDCVC model was established using the experimental results including total organic carbon (TOC), carbon element content in organic matter (OM), X-ray diffraction mineral composition analysis and low-pressure N2 adsorption/desorption (LPNA) tests, which were performed on three sets of subsamples. The PSDs associated with OM, clay, other components and shale sample per unit mass were obtained, and the PSDs of the subsamples calculated from PSDCVC method were compared with the results of LPNA and field emission scanning electron microscopy methods to confirm the credibility of PSDCVC results. For the shale samples from the same layer, the pore volumes (PV) of different pore widths associated with OM, clay and other components per unit mass are corresponding constants or similar to these constants, respectively. The PSDs associated with OM, clay and other components are primarily distributed in the pore widths of <5 nm, 20–100 nm and 10–100 nm, respectively. The PVs of pore widths <200 nm contributed by OM, clay and other components per unit mass are 1830.52 × 10−4 cm3/g, 29.52 × 10−4 cm3/g and 0.05 × 10−4 cm3/g, respectively. In the shale samples per unit mass, the average PVs of pore widths <200 nm contributed by OM, clay and other components are 49.16 × 10−4 cm3/g, 7.89 × 10−4 cm3/g and 0.04 × 10−4 cm3/g, representing contributed proportions of 85.80%, 14.14% and 0.06%, respectively. The PVs of pore widths <200 nm in the Wufeng Shale sample with TOC content >0.22% is mainly contributed by OM.