Methods: Soil was sampled (0–20 cm) from a 5-year Yellow River Delta paddy field experiment: no fertilizers (Control), mineral fertilizers (NPK), and NPK plus organic fertilizer (soybean and bean litter) applied at rates of 450 and 900 kg C ha− 1 (NPKC1 and NPKC2). The aggregate size, labile carbon fractions and root growth were investigated in combination with microbial community structure by high-throughput sequencing. Results: NPKC1 and NPKC2 fertilization decreased Na+ content, but increased available nitrogen, phosphorus and Ca2+ contents. Macroaggregate formation was increased under NPKC1 (by 28 %) and NPKC2 (by 62 %) fertilization through increase of labile carbon fractions (particularly microbial biomass carbon), as well as better root growth. NPKC1 and NPKC2 fertilization increased microbial diversity and enriched the microbial community towards taxa responsible for aggregate stability (e.g., Actinobacteria and Ascomycota). RDA revealed that dissolved organic carbon content was the main factor affecting microbial community composition. Conclusions: Combined mineral and organic fertilizers decreased Na+ content, increased macroaggregates due to broader microbial diversity, increased contents of labile organic carbon and Ca2+. Consequently, combined organic and mineral fertilization were the best practice to increase microbial biomass and labile carbon fractions that strongly contribute to aggregate formation in saline-alkaline soil. Aims: Soil structure is a key factor in sustainable agriculture, especially for saline-alkaline soils, because Na+ destroys clay minearls and colloids, and thus, prevents the aggregate formation. We assessed the effects of organic amendments in combination with mineral fertilizers on chemical properties, microbial community composition and aggregate formation in a typical saline-alkaline soil. © 2021, The Author(s), under exclusive licence to Springer Nature Switzerland AG.