CO2 leakage through the caprock of a CO2 sequestration site to the groundwater system is an important topic in the field of geo-environmental engineering. This problem can be described by a fully coupled model among the two-phase flow, caprock deformation, gas diffusion and CO2 sorption. The main purpose of this paper is to present such a model for investigating the caprock sealing efficiency. Firstly, a conceptual model is proposed for the flow in a composite body consisting of the fracture network and shale matrix. In this model, two-phase flow of brine water and CO2 is observed only in the fracture network but the CO2 in the fractures further diffuses into shale matrix through a much slower diffusion process. This diffusion process makes shale matrix swell/shrink through CO2 sorption and significantly alters the porosity and permeability of the fracture network. The interaction between the CO2-brine flow and shales induces shale deformation and modifies the sorptive chemistry of the shale matrix. Then, this conceptual model is formulated by the partial differential equations and full coupling of those processes, thus forming a fully coupled mathematical model. Finally, this fully coupled mathematical model is applied to a caprock layer to investigate the combined effects of two-phase flow, shale deformation, gas diffusion and CO2 sorption on the caprock sealing efficiency. The mechanism for self-enhancing or self-limiting in the CO2-brine mixing zone is explored. It is also applied to a caprock layer embedded a vertical fracture and the CO2 migration in the storage space. These examples demonstrate that this model is able to numerically simulate the CO2 storage relevant geological systems. This work may enrich the contents of the emerging computational geoscience discipline through geoscience modeling. © 2013 Elsevier B.V.