Graphene has attracted attention in the material field of functional microcapsules because of its excellent characteristics. The content and state of graphene in shells are critical for the properties of microcapsules, which are greatly affected by the charge adsorption equilibrium. The aim of this work was to investigate the effect of pH value on the microstructure and properties of self-assembly graphene microcapsules in regard to chemical engineering. Microcapsule samples were prepared containing liquid paraffin by a self-assembly polymerization method with graphene/organic hybrid shells. The morphology, average size and shell thickness parameters were investigated for five microcapsule samples fabricated under pH values of 3, 4, 5, 6 and 7. The existence and state of graphene in dry microcapsule samples were analyzed by using methods of scanning electron microscope (SEM), transmission electron microscope (TEM) and X-ray photoelectron spectroscopy (XPS). Fourier Transform Infrared Spectoscopy (FT-IR) and Energy Dispersive Spectrometer (EDS) were applied to analyze the graphene content in shells. These results proved that graphene had existed in shells and the pH values greatly influenced the graphene deposition on shells. It was found that the microcapsule sample fabricated under pH = 5 experienced the largest graphene deposited on shells with the help of macromolecules entanglement and electrostatic adherence. This microcapsules sample had enhanced thermal stability and larger thermal conductivity because of additional graphene in shells. Nanoindentation tests showed this sample had the capability of deforming resistance under pressure coming from the composite structure of graphene/polymer structure. Moreover, more graphene decreased the penetrability of core material out of microcapsule shells.