Deep shale gas has become a strategic alternative resource in China’s oil and gas energy portfolio. The core scientific challenges in the exploration and development of marine deep shale gas in the Sichuan Basin primarily include the formation mechanisms of shale reservoirs, the enrichment patterns of gas reservoirs, and multiphase/multiphysics-coupled seepage mechanisms. This study integrates experimental analysis with theoretical modeling, achieving the following breakthroughs. A CO2–N2—high-pressure mercury intrusion joint characterization technique based on density functional theory (DFT) was developed, enabling accurate quantitative characterization of full-aperture pores in deep shale. Nuclear magnetic resonance (NMR) T2 spectrum distribution technology was used to quantitatively analyze organic pores, inorganic pores, and microfractures in shale. Quantitative pore–fracture characterization revealed that the coupled effects of quartz compression–resistant pore preservation and reservoir fluid overpressure are key to the high porosity of marine deep shale in the Sichuan Basin. A novel paleotherm/pressure evaluation method was innovatively developed using laser Raman spectroscopy, fluid inclusion homogenization temperature measurements, and Sm‒Nd dating, enhancing the precision of paleothermobaric reconstruction during different uplift stages. Through laboratory experiments on shale adsorption‒desorption and molecular dynamics simulations, a new method for evaluating gas content was established. Integrating geological characteristics, the adsorption‒desorption behavior and main controlling factors of enrichment and accumulation in deep shale were clarified, confirming that free gas is dominant in deep shale gas reservoirs. By comprehensively considering adsorption/desorption, stress sensitivity, microscale flow, surface diffusion, and fracturing fluid effects, a multiphase/multimechanism seepage model was established, enabling dynamic predictions of gas‒water two-phase transient productivity in horizontal wells, characterization of complex fracture network distributions, and description of fracture parameter evolution during production. These technologies have played a crucial role in facilitating breakthroughs in the exploration of deep marine shale gas.