The past few decades have witnessed significant development in intercalation chemistry research aimed at precisely controlling material properties. Intercalation, as a powerful surface and interface synthesis strategy, facilitates the insertion of external guests into van der Waals (vdW) gaps in two-dimensional (2D) layered materials, inducing various modulation effects (the weakening of interlayer interactions, changes in electronic structures, interfacial charge transfer, and symmetry manipulation) to tailor material properties while preserving intralayer covalent bonds. Importantly, benefiting from the very diverse structures and properties of organic molecules, their intercalation enables the integration of various molecules with a wide array of 2D materials, resulting in the creation of numerous organic-inorganic hybrid superlattices with exotic properties, which brings extensive potential applications in fields such as spintronics, superconductor electronics, optoelectronics, and thermoelectrics. Herein, based on recent advancements in organic intercalation systems, we briefly discuss a summary and classification of various organic guest species. We also discuss three modulation effects induced by organic intercalation and further introduce intriguing modulations in physicochemical properties, including superconductivity, magnetism, thermoelectricity and thermal conductivity, chiral-induced spin selectivity (CISS) effects, and interlayer-confined chemical reaction. Finally, we offer insights into future research opportunities and emerging challenges in organic intercalation systems.