Commercial fertilizers and organic materials can alter aggregate distribution and aggregate-associated organic carbon (OC), total nitrogen (TN), and the C/N ratio. This study investigated the relationships between soil dry aggregate (DA) and water-stable aggregate and OC, TN, and C/N ratio as impacted by the long-term (1988–2009) application of chemical fertilizers, fertilizers plus rice straw (RS), and fertilizers plus pig manure (PM) in red soil in South China. Compared with those of the preexperiment in 1988, SOC was increased by 3.21 ± 0.55 g kg−1, 5.16 ± 0.62 g kg−1, and 5.77 ± 0.20 g kg−1, and TN was increased by 0.35 ± 0.04 g kg−1, 0.49 ± 0.03 g kg−1, and 0.61 ± 0.01 g kg−1 across 21 years for the control, RS, and PM treatments, respectively. The long-term application of PM significantly increased the macro-size DA (>0.25 mm) by 7.9% and water-stable aggregate by 5.9% because of higher soil OC and TN contents; RS, however, only increased DA by 4.9%. Addition of RS and PM influenced the C and N concentrations and C/N ratio in the aggregates, but there were no clear trends across aggregate size fractions. The contents of soil OC and TN were positively correlated with the amount of macroaggregates (>0.25 mm). Aggregate-associated OC was positively related to the aggregate-associated TN and C/N ratio. In general, PM had a greater effect than RS on the accumulation of soil OC and TN and the improvement of soil aggregation. Thus, long-term combined application of chemical fertilizer and organic materials, such as RS and PM, was an effective approach to enhance OC and TN accumulation in the bulk soil and aggregates, but the accumulation pattern was dependent on aggregate size.