Whispering gallery mode (WGM) microbubble cavities are a versatile optofluidic sensing platform owing to their hollow core geometry. To increase the light–matter interaction and, thereby, achieve higher sensitivity, thin-walled microbubbles are desirable. However, a lack of knowledge about the precise geometry of hollow microbubbles prevents us from having an accurate theoretical model to describe the WGMs and their response to external stimuli. In this work, we provide a complete characterization of the wall structure of a microbubble and propose a theoretical model for the WGMs in this thin-walled microcavity based on the optical waveguide approach. Structural characterization of the wavelength-scale wall is enabled by focused ion beam milling and scanning electron microscopy imaging. The proposed theoretical model is verified by finite element method simulations. Our approach can readily be extended to other low-dimensional micro-/nanophotonic structures.