Understanding how calcium carbonate (CaCO3) mediates soil aggregation and structure has important implications for soil organic carbon sequestration. Despite its prevalence in arid regions, the impact of CaCO3 on soil structure remains frequently overlooked and poorly understood. This study aimed to i) explore the relationships between organic and inorganic binding agents and soil aggregation across macro- to micro-scales, as indicated by mean weighted diameter (MWD), specific surface area (SSA), and porosity, and ii) assess the changes in SSA and porosity before and after CaCO3 removal in bulk soil and aggregate fractions. Conducting research along an elevation gradient in the Tianshan mountain, we evaluated soil aggregation indicators alongside organic binding agents (i.e., soil organic matter, SOM) and inorganic agents (i.e., CaCO3, exchangeable Ca, iron/alumina (hydro)oxides, and silt-clay). Our findings indicate that SOM primarily contributes to MWD, promoting macro-aggregate (>250 mu m) formation. The influence of SOM on SSA and total pore volume (TPV) varies with elevation sites, underscoring a SOM content-dependent relationship. Conversely, CaCO3 and exchangeable Ca form micro-aggregates in calcareous soils. Notably, CaCO3 exhibited a negative correlation with SSA and TPV, while its removal led to increased SSA and TPV in bulk soil and <53 mu m aggregates. This research highlights the divergent roles of SOM and carbonate in soil aggregation and their interactions in arid environments, emphasizing the importance of managing CaCO3 levels to maintain soil structure and organic carbon sequestration potential.