The development of the pore network during the thermal cracking of organic matter in shale plays an important role in the storage and transport of gas. There are several reports concerning the relationships between pore development and chemical composition in kerogen, however, little research has been performed to investigate how the transformation of the chemical structure affects the heterogeneous development of pores. In this study, kerogen isolation was performed on nine Longmaxi Formation shale samples with different maturities, then the chemical structure and pore development of isolated kerogens were studied using low-pressure gas adsorption, 13C Nuclear Magnetic Resonance spectroscopy, Raman spectroscopy, and high-resolution transmission electron microscopy. Results show that the reduction in micropores (< 2 nm pore diameter) at Ro 2, while the increase in micropores at Ro > 1.55% is primarily derived from the condensation of aromatic rings. The development of mesopores (2–50 nm) with increasing maturity could be the result of two different mechanisms: one is developed at the edges of the aromatic layers; another is formation in the space between structural clusters with different orientations. The development of mesopores is related to the compositions and disorder degree of chemical structure. Meanwhile, changes in chemical compositions can affect the surface and structural heterogeneities by altering the surface chemical properties and pore geometry, while variations in spatial arrangement only affect the structural heterogeneity by altering the distribution of void space. Transformation of the chemical structure not only reveals the inherent mechanism of pore heterogeneity in shale kerogens but also provides some microscopic insights for understanding the occurrence and transport behaviors of fluids.