The formation and stability of soil aggregates affect plant growth, carbon sequestration, and many other physiological and biogeochemical processes. Aggregates may be destabilized by nitrogen (N) deposition due to decreased inputs of binding materials; however, the legacy effects of which are unknown. An increase in labile carbon (C) input could mitigate the negative impacts of N addition on soil aggregate stability through the improvement of soil physical, chemical and biological conditions. Using a field experiment with the addition of NH₄NO₃ at multiple levels in a meadow steppe, we terminated the addition of N at the sixth year and shifted to applying labile C in the form of sucrose at three levels (C-0, C-200, and C-2000 g C m⁻² y⁻¹) to soil for two years. Then we examined the aggregate size distribution and the associated soil properties. The high historical N addition rates decreased the proportion of macroaggregates (>2000 μm) and increased microaggregates (<250 μm), leading to a reduction in the mean weight diameter (MWD), an index of soil aggregation stability. Labile C input offset the legacy effects of N addition on soil aggregates hierarchy and reversed the N-induced changes in MWD. Labile C input did not affect soil pH and exchangeable Ca²⁺, but increased the microbial biomass carbon (MBC) and the relative abundance of soil saprotrophic fungi (SSF); whilst the C-200 increased the relative abundance of arbuscular mycorrhizal fungi (AMF) only at low N addition rates (<N₂₀) in comparison with that of the C-0. Analysis with the structural equation model (SEM) revealed the positive effects of labile C input on soil aggregate stability mainly by increasing the relative abundance of SSF across all N addition rates. The results of this study clearly demonstrate the effective role of short-term (2 years) labile C input in offsetting the N-caused soil aggregate instability in the meadow steppe by promoting soil microbial activity.