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Highlights • This study focused on soil aggregates and nutrients in fen with different layers. • Soil aggregate structure exists in fen soil. • Soil aggregate structure important in soil nutrient cycling similar in upland soil. • Macroaggregates have a strong relation with carbon sequestration. • Stable soil microaggregates are important for nutrient conservation in this fen. Abstract Soil carbon and nutrients play vital roles in ecosystem services. Many previous studies documented carbon or nutrient accumulation and the relevant impacting factors, and emphasized the soil physical structure, especially soil aggregates, that might play a key role in grasslands or farmlands. Unfortunately, there is little known about the relationship between soil aggregates and nutrient sequestration in fens and which soil aggregate type contributes most strongly to the soil nutrient cycle in fens. In this study, we collected 180 soil samples from 3 sites and then tested the changes in soil nutrient contents and carbon sequestration rates based on soil aggregate fractions from a fen that has critical implications for temperate wetland ecosystems in Northeast China. This fen soil is obviously characterized with macroaggregate and microaggregate structures. For this soil, the mean weight diameter (MWD) ranged from 0.42 to 0.61 mm and the geometric mean diameter (GMD) ranged from 0.82 to 0.90 mm, and there were fluctuations for both MWD and GMD along with soil depth. The correlation analysis showed that macroaggregates were more closely related to carbon sequestration (p < 0.01) and stable soil microaggregates were important for nutrient conservation (p < 0.01) in this fen. The sequestration rates of carbon, nitrogen and phosphorus were 87.64 ± 10.88 gC m−2 yr−1, 3.43 ± 0.54 gN m−2 yr−1, and 0.17 ± 0.02 gP m−2 yr−1, respectively. Additionally, the characteristic stoichiometric balance was related to the aggregate size and there were four distinct intervals for both the C/N ratio and C/P ratio; three intervals were located in similar ranges for the C/N ratio and C/P ratio (12–14 cm, 20–22 cm, and 28–30 cm) which means three of these areas coincided with the C/P ratio that characterizes the phosphorus conversion intensity index. The findings indicate that soil aggregates play key roles in soil carbon sequestration and nutrient cycling within wetlands. [ABSTRACT FROM AUTHOR]