Practically quantifying gas-in-place content in organic matter (OM)–hosted and mineral-hosted pores is essential to understanding shale gas storage and recovery mechanism, and this remains challenging by conventional methods. This study obtained different porosity type and pore size distribution by integrating scanning electron microscopy and helium ion microscopy image analysis and CO2 adsorption experiments. Based on detailed porosity data and a nonlinear multiple regression model of methane-adsorbed density, adsorbed- and free-gas content of OM-hosted pores and mineral-hosted pores were estimated for the most gas-productive marine Silurian Longmaxi shales in the Sichuan Basin, China. Results show that the gas-in-place volume of 14 wells with producing depths of 387 to 4334 m (1270 to 14,219 ft) ranges from 1.9 to 7.9 m3/t (67 to 279 SCF/ton), and OM is the main gas storage site. The total gas content increases first and then remains relatively stable at depths greater than 3500 m (11,482 ft). Compared to deep shales with free-gas percentages of more than 60%, the shallow shales especially lower than 500 m (1640 ft) are dominated by adsorbed gas. The depth-dependent gas-bearing properties are suggested to be coupling results of reservoir pressure conditions and pore characteristics by tectonic uplifts. The gas recovery across pore size at different production pressures was further estimated, and a higher ultimate production was found at higher depths. Our proposed model provides important insights for gas occurrence in nanopores, and it is significant for an accurate gas-in-place estimation and production prediction for deep shales.