Better understanding of the role of soil structure, e.g., arrangement of soil aggregates and inter-aggregate pores, in carbon (C) sequestration can be achieved by coupling soil incubation studies with X-ray computed micro-tomography (CT) scanning. CT is a non-destructive technique that has been successfully used for three-dimensional examination of intact as well as disturbed soil samples. The objective of this study is to examine the influence of pore size distribution characteristics on mineralization of soil C and decomposition of plant residue added to soil. Soil collected from depths of 0-15 cm in a conventionally managed cropping system at the Long Term Ecological Research site at W. K. Kellogg Biological Research Station was used for this study. Soil samples with five contrasting pore size distributions were built by using aggregates of five different sizes, namely <53, 53-105, 105-500, 500-1000 and 1000-2000 µm. The samples were incubated for 120 days and soil respiration was measured on the samples at regular time intervals. To assess the effect of pore structure on decomposition of plant residue, a piece of dry maize leaf was added to half of the studied samples. The samples were subjected to CT scanning before and after incubation. In order to ensure that the observed differences stem from the differences in pore structures rather than the inherent properties of the aggregates of different sizes, ground samples of each aggregate size was subjected to incubation with and without maize leaf amendment. CT image analysis demonstrated that a higher proportion (~72%) of the added maize leaf was decomposed in samples with greater presence of large (>100 micron) pores, i.e. in 1000-2000 and 500-1000 µm aggregate samples, while only 40-60% of the leaf was decomposed in samples with pore distributions dominated by small pores. Overall, the proportion of decomposed leaf was positively related to the maximum size of the pores present in the sample with a regression model explaining 79% of variations in leaf decomposition. Total C (TC), total nitrogen, and cumulative C mineralization were significantly (P<0.05) higher in 53-105 µm aggregates as compared to aggregates of other sizes. However, grinding increased cumulative C-mineralization 2.64 and 1.44 fold in 1000-2000 and 500-1000 µm aggregate sizes, respectively, as compared with unground of the same size without leaf amendments. In general, smaller aggregate samples were higher in TC concentration while larger aggregates were higher in protected C and also experienced a higher rate of plant residues decomposition.