Compound microbubbles with engineered shells, fabricated by microfluidic techniques, have drawn considerable interest for interdisciplinary research, including ultrasound imaging agents, chemical micromotors, and optical microcavities. Meanwhile, though vastly investigated, dynamic shell thickness variations of microbubbles can be hardly calculated via conventional techniques. Here the fabrication of colorful microbubbles encapsulated in hydrogel precursor using glass‐capillary microfluidic methods is demonstrated. The proposed optical geometrical model elucidating the structural coloration is used for thickness assessment. Thin‐film interference occurring upon illumination of the microbubble shell is found to be responsible for the coloration. The interfered lights travel along with the shell interfaces through total internal reflection in microbubbles with buoyancy‐induced asymmetric shell. A concise thickness evaluation methodology provided by the established model predicts the thickness evolution of microbubbles. These results demonstrate tunable optical properties of shin‐shell compound microbubbles for potential applications in displays, sensing, and anti‐counterfeiting materials.