To investigate the effect of aggregate size on pore structure and pore evolution in water saturation of manufactured sand aggregate (MSA) mortars, five MSA mortars with small range of aggregate sizes were prepared and their pore characterization were monitored over 365 days. The findings showed that an increased surface volume ratio (SVR) leads to an increase in total and macroporous porosity, and three pores with different connectivity were quantified using double T2 cutoff method. Moreover, continued hydration by unhydrated cement caused an increase in micropores during the initial stage of service in a water-saturated environment for 365 days, and an increase in macropores at the later stage as a result of enhanced hydraulic solvation, furthermore, solvation was more significant in the mortar with larger SVR to the point where it eventually produced pores larger than 100 μm. This research would provide guidance for the durability evaluation of cement mortars.