The common microscale to nanoscale pore types were introduced and divided into organic and inorganic pores to estimate their contributions to porosity in the Lower Silurian Longmaxi Formation shale of southeast Chongqing. Following the material balance principle, the organic porosity values, which changed with formation subsidence and thermal evolution, were calculated using chemical kinetics methods and corrected via the organic porosity correction coefficient, which was obtained from field emission scanning electron microscopy. Grain density values were determined using the contents and true densities of compositions in the shale samples. The total porosity was calculated based on the grain and bulk densities. The inorganic porosity was determined from the difference between the total porosity and organic porosity at the same depth. The results show that inorganic pores mainly contain microfractures, microchannels, clay intergranular pores, intercrystalline pores and intracrystalline pores in the Lower Silurian Longmaxi Formation shale of southeast Chongqing. Organic pores mainly include organopore and fossil pore. The total porosity, organic porosity and inorganic porosity of organic-rich shale samples can be quantitatively evaluated using this method. The total porosity, organic porosity and inorganic porosity values of the Longmaxi Formation shale samples from the well Py1 in southeast Chongqing lie in 2.75%–6.14%, 0.08%–2.52% and 1.41%–4.92% with average values of 4.34%, 0.95% and 3.39%, respectively. The contributions of the inorganic pores to the total porosity are significantly greater than those of the organic pores.