To understand the waterflooding mechanism in low-permeability cores, the CT scanning has been applied to monitor the in-situ water saturation profiles along the core at different time points. The new method improves the accuracy of measurement with CT values correction. The influence of injection rates (or capillary numbers), presence of connate water and heterogeneity of core samples on displacement characteristics of waterflood has been further studied. The saturation profiles show convective straight displacement at high flow rate (high capillary number) that is, the piston-like transport mechanism is favorable. While at low flow rate (low capillary number), the capillary forces broaden the saturation distribution and water breakthrough occurs at the outlet very quickly which makes the snap-off and crawling mechanism predominant. The presence of connate water lessens the steepness of imbibition fronts. It could be attributed to the pre-existing water phase in the small pores which supplies wetting fluid and forms the stable collars of water before the connected front catches up. Therefore, the presence of connate water promotes snap-off events. The advance of saturation front proceeds in a hyper-dispersive manner and the saturation profiles are almost uniformly distributed along the heterogeneous core samples.The microscopic heterogeneity increases the difference of capillary forces generated in the displacing process, which causes the bypassing and fingering to be the dominant oil entrapment mechanism.