Optical microcavities, which support whispering gallery modes, have attracted tremendous attention in both fundamental research and potential applications. The emerging of two-dimensional materials offers a feasible solution to improve the performance of traditional microcavity-based optical devices. Besides, the integration of two-dimensional materials with microcavities will benefit the research of heterogeneous materials on novel devices in photonics and optoelectronics, which is dominated by the strongly enhanced light–matter interaction. This review focuses on the research of heterogeneous two-dimensional-material whispering-gallery-mode microcavities, opening a myriad of lab-on-chip applications, such as optomechanics, quantum photonics, comb generation, and low-threshold microlasing.