Manufactured sand served as the substitute for natural sand for concrete ingredients has been an increasingly common trend nowadays for sustainable development in the concrete industry. The stone powder of manufactured sand poses an impact on its porosity. The differences of pore structure between concretes determine the strength and durability directly. In order to research the filling effect caused by different contents and particle sizes of stone powder on pore structure, several concrete cubes with manufactured sand were made, considering stone powder (a substitute of cement) of different contents (0%, 5%, 10%, 15%, 20%), also different particle sizes (400 mesh, 600 mesh, 800 mesh, 1250 mesh, 2000 mesh, 3000 mesh). Then a dual-source CT was operated to obtain the figures for macroscopic porosity of curing time at 3 days, 7 days, 14 days, and 28 days. Finally, the cubic compressive strength of 28-day concrete was tested by the compressive strength experiment. The result illustrated that the strength of concrete made of manufactured sand was positively associated with its porosity to a certain extent. The content as well as the particle size of stone powder and curing time of concrete differentiated between effects on its porosity. Ideal improvement of the pore structure was carried out when the particle size of the stone powder was 1250 mesh and the content of stone powder was 15%. The characteristics of stone powder enable us to optimize the porosity of concrete made by manufactured sand while reducing the consumption needed of cement.