The addition of biochars produced by different feedstocks to soil affects soil aggregation, which has been shown to be critical for soil carbon sequestration, water holding capacity and plant growth. In this study, rice stalk biochar (RB) and canola stalk biochar (CB) produced at 350℃ were added to a Ultisol at the 1% rate. After a three-year incubation, the macroaggregates (5–6 mm) in soils were separated for quantification of pore structure using industrial X-ray computed tomography (CT) scanning. The RB and CB treatments significantly increased the total porosity and the ratio of connectivity to isolated porosity(C/I) in macroaggregates relative to CK treatments. The addition of biochars decreased the proportion of equant pores in the macroaggregates, while increased the proportion of irregular pores such as prolate and acircular pores, resulting in the high porosity heterogeneity in macroaggregates. The canola stalk biochar had a larger effect on the improvement of pore structure than rice stalk biochar, while having the opposite effect on pore throat structure. There was a positive correlation between porosity, connectivity and SOC in macroaggregates. Simulation results on water flow showed that the permeability for RB and CB treatments were 25.16 μm2 and 28.62 μm2, respectively, which were 116.7% and 146.5% higher than that of CK treatment (11.61 μm2). The results indicated that the biochars altered the pore structure of macroaggregates, potentially enhancing the functional services of macroaggregates such as SOC storage and hydraulic properties. The findings provided the detailed information on the effect of different biochar additions on pore structure in macroaggregates and simulated soil water movement within the macroaggregates, which is important for understanding the mechanism of biochars affecting soil aggregation and its functions.