Abstract This study analyzed self-healing microcapsules composed of melamine, urea, and formaldehyde (MUF). The thin shell’s mechanical properties were predicted using various techniques to gain a comprehensive understanding of their behavior. The compressive behavior of the microcapsules was assessed through micro-compression testing. The elastic modulus of the thin shell was precisely determined using nanoindentation, a method known for its accuracy in measuring material properties. Finite element analysis (FEA) was then applied, modeling the microcapsule between two plates and treating the core, which contains the healing agent, as an incompressible liquid. The mechanical properties of the thin shell, based on the elastic modulus derived from the nanoindentation test, were incorporated into the FEA, and the results were compared with those from the micro-compression test. Additionally, we analyzed the von Mises stress distribution to evaluate stress concentration within the spherical core–shell structure, ensuring the reliability of our conclusions. The test methods and analysis techniques presented in this study provide guidelines for improving the stiffness of MUF microcapsules. They can be further applied to predict the properties of materials with a spherical core–shell structure.