In view of strong heterogeneity and complex formation and evolution of organic pores, field emission scanning electron microscopy (FESEM), Raman spectrum and fluid injection + CT/SEM imaging technology were used to study the macerals, organic pores and connectivity of organic pores in the lower Paleozoic organic-rich shale samples from Southern China. Combined with the mechanism of hydrocarbon generation and expulsion and pore forming mechanism of organic matter-based activated carbon, the relationships between organic pore development and the organic matter type, hydrocarbon generation process, diagenesis and pore pressure were explored to reveal the controlling factors of the formation, preservation and connectivity of organic pores in shale. (1) The generation of organic pores goes on through the whole hydrocarbon generation process, and is controlled by the type, maturity and decomposition of organic matter; the different hydrocarbon generation components and differential hydrocarbon-generation evolution of kerogen and solid asphalt lead to different pore development characteristics; organic pores mainly develop in solid bitumen and hydrogen-rich kerogen. (2) The preservation of organic pores is controlled by maturity and diagenesis, including the steric hindrance effect of in-situ hydrocarbon retention, rigid mineral framework formed by recrystallization, the coupling mechanism of pore-fluid pressure and shale brittleness- ductility transition. (3) The Ro of 4.0% is the maturity threshold of organic pore extinction, the shale layers with Ro larger than 3.5% have high risk for shale gas exploration, these shale layers have low gas contents, as they were in an open state before uplift, and had high hydrocarbon expulsion efficiency and strong aromatization, thus having the “congenital deficiency” of high maturity and pore densification. (4) The pores in the same organic matter particle have good connectivity; and the effective connectivity between different organic matter pores and inorganic pores and fractures depends on the abundance and distribution of organic matter, and development degree of pores and fractures in the shale; the accumulation, preservation and laminar distribution of different types of organic matter in high abundance is the prerequisite for the development and connection of organic pores, grain margin fractures and bedding fractures in reservoir.