The self-healing system based on microencapsulated epoxy-amine chemistry is currently the self-healing system with the most practical application potential. It can be widely used in many epoxy-based materials with a size restriction for the microcapsules, such as fiber-reinforced composites, anti-corrosion coatings, etc. Although epoxy microcapsules of different sizes can be fabricated using different techniques, the preparation of polyamine microcapsules with suitable sizes and good performance is the prerequisite for further developing this self-healing system. In this investigation, based on the novel microencapsulation technique via integrating microfluidic T-junction and interfacial polymerization, the feasibility of preparing small-size polyamine microcapsules and the process regulation to optimize the properties of the small-size microcapsules were studied. We show that polyamine microcapsules with sizes smaller than 100 μm can be obtained through the T-junction selection and the feeding rate control of the polyamine. To regulate the small-size microcapsules’ quality, the effects of the concentration of the shell-forming monomer and the solvent with different polarity in the reaction solution and the reaction condition were studied. It shows that dry, free-flowing small-size microcapsules can still be obtained when the shell-forming monomer concentration is higher and the solvent’s polarity is lower, compared with the preparation of larger polyamine microcapsules. Although the change of reaction conditions (reaction temperature and duration) has a certain effect on the microcapsules’ effective core content, it is relatively small. The results of this investigation further promote the potential application of the self-healing systems based on microencapsulated epoxy-amine chemistry in materials with a size restriction for the microcapsules.