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Soil aggregate stability is an important property for soil carbon sequestration and many other soil functions, but the co-impacts on soil aggregates from nitrogen (N) deposition and precipitation change (two important features of global climate changes) remain unknown. In this study, N addition and throughfall reduction were implemented in a Korean pine forest through a total of four treatments, control (CK), throughfall reduction (TR), N addition (N50) and throughfall reduction plus N addition (TR-N50). Plant root traits, glomalin-related soil proteins (GRSPs), soil properties and soil aggregates were investigated to explore how these treatments influenced soil structure. The results showed that six-year N addition and throughfall reduction had no significant effect on pH, carbon to nitrogen ratios (C/N ratios), microbial biomass carbon (MBC) and bulk density (BD), but an interactive effect of N addition and throughfall reduction on dissolved organic carbon (DOC) and soil organic carbon (SOC) was recorded. Root traits, such as root length density (RLD) and root weight density (RWD), decreased in the TR and TR-N50 plots compare with CK, especially RLD, which decreased by approximately 47.28% and 20.32%, respectively. GRSPs released from AMF associated with fine roots obviously decreased in the TR and TR-N50 treatments especially for total glomalin-related soil protein (TGRSP). Similar trends were observed for the proportion changes of > 2 mm macroaggregates, whereas contrasting trends were observed for < 2 mm aggregates in response to experimental treatments, resulting in decreased MWD in the TR-N50 treatment. These results indicated that the negative interactive effects of N addition and throughfall reduction on soil structure were mainly associated with biological binding agents (especially GRSPs), based on evidence from principal component analysis and Pearson correlations. Therefore, our results suggest that biological binding agents will strongly mediate soil aggregation under the perspective N deposition and precipitation change.