In this paper, geomechanics is coupled with reservoir flow for modeling the depletion and deformation in fractured vuggy carbonate reservoir. Different from the dual- and triple-porosity models or the coupled approaches in which the vugs are considered as a continuous porosity, the vugs are treated as virtual volumes in this study. For each vug, the fluid exchange at the vug-matrix interface is dynamically calculated with time evolution and the pore pressure in the vugs is updated through considering both the fluid material balance and the volume change due to the mechanical deformation of vug. The fluid-mechanical interaction in the rock matrix and natural fractures is calculated based on the framework of Biot's poroelstic theory. The mechanical and hydraulic interactions between vugs and matrix are preserved and the stress evolution due to the depletion can be dynamically updated. The results in this study show that, the depletion process is mainly controlled by the fluid storage of the vugs. Fluid modulus is thus a more sensitive parameter than the rock/fracture modulus in terms of the depletion. However, the rock/fracture modulus can also affect the deformation of the system and thus affect the volume and pressure changes of the vugs.