Abstract Whether flowback bottom water can form effective traps has a significant effect on the effective sequestration of injected supercritical carbon dioxide (SC–CO2) in anticline reservoirs. An in-depth core flooding experiment was conducted to investigate the flow behavior characteristics of SC-CO2 in a heterogeneous tight glutenite sample. Three NMR/MRI pulse sequences (CPMG, GR-HSE and SE-SPI) were used to monitor the flooding processes. The CPMG pulse sequence provided T2 spectra for the whole sample and the results show that the injected fluid always displaced the initial existing fluid from the larger macropores first. However, as water could form thin films on the pore surfaces or isolated beads in the middle of pores, the T2 spectra did not truly reflect the water distribution in different size pores during the drainage and imbibition processes. The GR-HSE sequence gave the saturation profiles as a function of lateral position along the core allowing the migration front of fluid along the flooding direction to be determined. These profiles provided direct evidence of the different influence of viscosity difference between SC-CO2 and water causing on heterogeneity-induced fingering during the drainage and imbibition processes. During the imbibition process, the extent of viscous fingering was reduced significantly. The SE-SPI sequence gave the T2 spectra for individual layers and provided a new perspective to determine the partial wettability of these layers. MRI imaging shows that the drainage and imbibition processes occurred mainly in the matrix, while the gravels were largely devoid of fluids. The displacement efficiencies during drainage and imbibition processes (calculated by averaging the values obtained from the CPMG and GR-HSE sequences) were 65.6% and 92.3%, respectively.