In order to promote the application of MgO concrete, the microstructure of MgO cement-based materials (cement mortar and one-grade concrete mortar) of small-size autoclave-treated specimens was investigated using mercury intrusion porosimetry and scanning electron microscopy. The results show that with the change in specimen size, the average pore diameter of MgO cement-based materials of micro specimens is the largest, followed by small specimens and standard specimens. The proportion of harmless and less harmful pores of standard specimens is the largest, followed by small specimens and micro specimens. With the same amount of MgO, as the amount of fly ash increases, the standard specimens have the smallest average pore diameter and the highest proportion of harmless and less harmful pores compared to small and micro specimens.