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The intercropping of maize (Zea mays L.) and peanuts (Arachis hypogaea L.) (M||P) significantly enhances crop yield. In a long-term M||P field experiment with two P fertilizer levels, we examined how long-term M||P affects topsoil aggregate fractions and stability, organic carbon (SOC), available phosphorus (AP), and total phosphorus (TP) in each aggregate fraction, along with crop yields. Compared to their respective monocultures, long-term M||P substantially increased the proportion of topsoil mechanical macroaggregates (7.6–16.3%) and water-stable macroaggregates (>1 mm) (13.8–36.1%), while reducing the unstable aggregate index (ELT) and the percentage of aggregation destruction (PAD). M||P significantly boosted the concentration (12.9–39.9%) and contribution rate (4.1–47.9%) of SOC in macroaggregates compared to single crops. Moreover, the concentration of TP in macroaggregates (>1 mm) and AP in each aggregate fraction of M||P exceeded that of the respective single crops (p < 0.05). Furthermore, M||P significantly increased the Ca2-P, Ca8-P, Al-P, and Fe-P concentrations of intercropped maize (IM) and the Ca8-P, O-P, and Ca10-P concentrations of intercropped peanuts (IP). The land equivalent ratio (LER) of M||P was higher than one, and M||P stubble improved the yield of subsequent winter wheat (Triticum aestivum L.) compared with sole-crop maize stubble. P application augmented the concentration of SOC, TP, and AP in macroaggregates, resulting in improved crop yields. In conclusion, our findings suggest that long-term M||P combined with P application sustains farmland productivity in the North China Plain by increasing SOC and macroaggregate fractions, improving aggregate stability, and enhancing soil P availability. [ABSTRACT FROM AUTHOR]