Background and aims Soil aggregate stability is profoundly influenced by elevated atmospheric nitrogen (N) deposition, although the mechanisms remain elusive. Here we evaluate the role of microbial-derived soil organic carbon (SOC) of different origins in mediating soil aggregate stability under N addition. Methods We conducted an N addition experiment with three-level (0, 8, and 40 kg N ha(-1) yr(-1)) in a subalpine forest to study the alteration of soil aggregate stability using mean weight diameter (MWD) and geometric mean diameter (GMD) as proxies. SOC content of aggregates, glomalin-related soil proteins (GRSP) and amino sugars were measured to indicate SOC associated with aggregates, derived from arbuscular mycorrhizal fungal hyphae and microbial necromass, respectively. The relative importance of these factors in regulating aggregate stability were explored using multivariate analysis. Results Nitrogen addition tended to enhance the stability of soil aggregates. In the top 5 cm soil, the N addition level of 40 kg N ha(-1) yr(-1) significantly (p < 0.05) increased MWD and GMD by 99% and 43%, respectively. Contents of aggregate-associated SOC, microbial necromass, and easily extractable GRSP also increased under N addition and positively correlated with the aggregate stability. Both the aggregate-associated SOC and the easily extractable GRSP (E-GRSP) exerted a direct impact on the stability of soil aggregates. Amino sugars, along with E-GRSP, indirectly influenced soil aggregate stability via their effects on aggregate-associated SOC. Conclusion Nitrogen addition improves soil aggregate stability by increasing the contents of soil microbial gluing agents. Compared to microbial necromass, fungal hyphae tend to play a more significant role in regulating soil aggregate stability.