Although CO2 injection into the geological formations is a promising option to enhance oil recovery, the effect of multiscale pore structures in porous media on multiphase fluid transport remains poorly understood. This study leverages the unique advantages of real-time in-situ visualization of microfluidics to investigate multiphase flow behavior in micro and nano-pores during both CO2 miscible and immiscible flooding process. The nanoporous media chips with microchannels fracture structure were designed to investigate the impact of both fracture-matrix interaction and CO2 flooding method on the multiphase flow patterns and the recovery rates throughout the entire CO2 flooding process. In CO2 miscible flooding, fracture microchannels expedite the process of achieving the 100% recovery rate. Conversely, in CO2 immiscible flooding, the fracture microchannels provide a “short circuit” pathway for CO2, resulting in the extensive entrapment of residual oil and a substantial reduction in the recovery rate. These results enhance our understanding of the impact of heterogeneity on multiphase transport in CO2 enhanced oil recovery, thereby facilitating the optimization of practical CO2-EOR schemes.