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Fertilizer application is important to achieve sustainable agriculture. However, it remains unclear about the effects of long term fertilization on C and N immobilization as well as C/N ratios in soil aggregates at different depths. Samples taken at depths of 0 to 40 cm from dryland red soil subjected to long-term fertilization were analyzed. Four treatments were involved in the long term fertilization including no fertilizer (control), chemical fertilizer applied at two different rates, and manure combined with chemical fertilizers (MNPK). The C and N concentrations in the soil aggregates of different sizes were significantly higher (P &lt; 0.05) and the C/N ratios in the particulate organic matter were significantly lower (P &lt; 0.05) for soil to 20 cm deep for the MNPK treatment than for the other treatments. ANOVA indicated that the C and N concentration and C/N ratios in different sizes of aggregates significantly varied with soil depth (P &lt; 0.05). Microaggregates contained most of the C and N, and the C/N ratios for silt–clay particles in macroaggregates were 1.37 unit (ranging − 0.25 to 2.44) lower than for other soil particles with diameters &lt; 53 µm. The C and N contents in aggregates of different sizes increased as the C input rate increased to a depth of 40 cm because of the fertilization practices. Overall, both increased C input and deep application of C sources promoted the storage of C and N in microaggregates, which in turn increased C and N sequestration in dryland red soils.

Differences in total stored C and N in dryland red soil caused by different long-term fertilization practices