For greenhouse gas control and environment protection, CO2 emission reduction has become a hot spot in global research. CO2 injection in developed oil reservoirs to enhance oil recovery is widely regarded as one of the most economical and promising measures for reducing anthropogenic CO2 emissions into the atmosphere. In this paper, a three-dimensional embedded discrete fracture model is proposed and applied to simulate CO2 flooding and geological storage processes in hydraulically fractured reservoirs. The gas injection is simplified as a two-phase two-component mathematical model with the varying pressure-related fluid physical properties, and its accuracy is verified by commercial software tNavigator®. The advantage of this model is that it can deal with the complex geological conditions of three-dimensional arbitrary-inclined fracture networks and accurately assess the effects of CO2-EOR and geological sequestration in real reservoirs. Two application cases of CO2 huff-and-puff with a single well and inter-fracture asynchronous injection and production are demonstrated and explained in detail. The optimized technological parameters and CO2 saturation distribution can provide key technical parameters for field operations.