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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. [ABSTRACT FROM AUTHOR]

• Biochar significantly increased the sequestration of SOC in saline soil. • Macroaggregate in organic fertilizer and straw were higher than that in biochar. • CMI values was greater in straw compared with organic fertilizer and biochar. • Organic amendments affected exchangeable cation distribution in aggregates. Organic amendments are a recyclable resource and can improve soil quality and carbon (C) sequestration, however, the difference in their effects on soil aggregate formation and C sequestration in saline-alkaline soils are less studied. We examined the effects of organic amendments to saline rice paddy fields with 4 treatments: (i) basal paddy soil (CK) lacking amendments (ii) organic fertilizer (OF) treatment at 910 kg C ha−1 from soybean litter and beans (iii) rice straw (RS) treatment at 3600 kg C ha−1 and (iv) rice straw-derived biochar (RS-biochar) treatment at 3600 kg C ha−1. All organic amendments significantly increased the soil organic C (SOC) stock in the 0–30 cm soil layer compared to CK. The SOC stock in the biochar treatment increased by 6.2 and 40.4% over the OF and RS amended treatments, respectively. This was most likely due to the greater levels of aromatic C in RS-biochar at 1.22 and 1.24 times greater than for the other organic amendments, respectively. Soil aggregates of 2–8 mm at 0–15 cm in the OF and RS amended soils were 38.3 and 58.2%, respectively, higher than that from the RS-biochar treatment. The mean weight diameter (MWD) in the OF and RS treatments were 35.4% and 45.8% higher than for the RS-biochar, respectively. MWD was significantly negatively correlated with soil exchangeable Na (p < 0.05). This indicated OF and RS were better than RS-biochar in improving soil aggregate stability. In addition, the C management index values for RS were 21.6 and 45.8% greater than for OF and RS-biochar in the 0–15 cm soil layer, respectively. These data indicated that saline soil aggregate formation and C sequestration improved after organic amendments application, which caused the exchangeable Na to decrease and affected its distribution in aggregates, and changed the composition of C functional groups. [ABSTRACT FROM AUTHOR]