Planting patterns and agricultural practices, such as fertilization, influence soil aggregate stability and SOC concentration [
14,
29]. In this study, long-term M||P significantly increased SOC concentration in macroaggregates, developed the proportion of mechanical and water-stable macroaggregates, and had a strong positive effect on soil aggregation (Figure 2 and Figure 3). These findings support our first hypothesis and are consistent with previous studies [
5,
31,
42]. Intercropping is an important cultivation method that increases C input by increasing aggregate stability [
24,
28], which can improve organic matter persistence in agricultural soils by maximizing biodiversity [
4], improving aboveground productivity and underground biomass, strengthening interspecific edge effects [
43], changing the soil microbial community structure, reducing pathogenic bacteria, and increasing plant rhizosphere vitality, all of which are conducive to soil C sequestration and storage [
11]. Intercropping of sugarcane with other crops increases organic C sources that can replenish organic C in aggregates directly, with organic C encapsulated in aggregates or existing in pores in the form of particles, which reduces organic C decomposition [
44]. Studies have shown that long-term faba bean-maize intercropping can improve the microbial community structure in crop rhizosphere soil, increase fungal biomass, and stimulate microorganisms to release cementing substances [
25]. These cementing substances, released by microbial communities, play a crucial role in soil structure development by binding primary soil particles into larger aggregates [
45]. Soil macroaggregates are composed of microaggregates and organic matter, so an increase in macroaggregates results in a gradual rise in soil organic carbon [
46]. However, Zhou et al. [
47] demonstrated that intercropping could increase soil microaggregate fractions and reduce soil aggregate mean weight diameter (MWD), while Peng et al. [
12] found no significant difference in the proportion of aggregates between sole cropping and intercropping. Some studies suggest that as plant diversity increases, litter decomposition rates become slower than input rates, which can increase total soil organic carbon (SOC) while reducing the soil’s active carbon pool [
48]. Importantly, the formation of soil aggregates and changes in SOC are long-term and gradual processes. Factors such as test duration, soil type, crop type, and climatic conditions can significantly influence research outcomes [
5,
25].
In addition to the direct effects of intercropping, P application significantly influenced aggregate-associated C and aggregate stability. Fertilizer type and planting pattern influence both the degree of soil aggregation and the fate of C stability in agroecosystems [
49,
50]. This study concludes that P application significantly increased aggregate stability and SOC concentration (Table 1, 3 Figure. 3A). The results align with the findings of Prakash et al. and Bansal et al. [
51,
52], who also observed that P application promotes soil enzyme activity and enhances SOC concentration [
51,
53]. Phosphate fertilizer application fosters crop growth and development and substantially increases crop biomass and soil microbial biomass C, thus contributing to soil C sequestration [
53] (Mahmoud et al. 2019). Moreover, P fertilizer can enhance C sequestration by stimulating microbial activity and root biomass, thereby promoting the formation of soil aggregates [
54,
55]. In cases of low-P soils, the appropriate application of P fertilizer can result in increased SOC and nitrogen storage and the development of macroaggregates (> 2 mm) [
52]. In high-P soils, rhizosphere interactions in intercropping systems can enhance soil aggregation and boost C sequestration. These effects are primarily driven by physical root contact, with secondary contributions from biochemical activities [
14].