Steam flooding is widely used in heavy oil development. The temperature in the steam chamber during the development process can be as high as 280°C, which will change the micro-scale pore structure of the core. In this paper, two types of heavy oil reservoir cores with different clay content, i.e., argillaceous glutenite and siltstone derived from Shengli Oilfield in China, are used to carry out steam flooding experiments. The micro-CT online scanning system was used to scan the two cores before and after steam flooding in situ, the scanned images were processed and the pore network models were established, and the mean, skewness and kurtosis of the pore throat radius were compared. After steam flooding, the number of pore throats with smaller radius in the siltstone decreases, and the distribution of pore throat radius is more dispersed. The number of pore throats with small radius of argillaceous glutenite increased after steam flooding, and large pores appeared. The average pore throat radius of the two cores increased after steam flooding, and the increase of argillaceous glutenite was greater. It shows that rock particles will expand and clay minerals will dehydrate at high temperature, and the latter plays a dominant role, and cores with high amounts of clay content are more susceptible to temperature. Noticeably, the solid particles in the siltstone may be dissolved at high temperature, which increases the connectivity of the microscopic pore throats. Solid particles in argillaceous glutenite migrate under the mechanical force of steam and condensate, and may block pores and throats. This leads to irregular changes in the pore-throat structure, and it is easy to produce sand to form microscopic steam channeling paths in the reservoir. The microscopic pore-throat structure change law of the reservoir after steam flooding is important for understanding the mechanism of steam channeling paths; and more importantly, it is useful for the optimization of steam channeling prevention technology for thermal oil recovery in heavy oil reservoirs.