Objectives This study aimed to clarify the effects of silicon fertilizer on cotton nitrogen (N) uptake, soil N fractions, and microbial N-cycling functional potential under salt and alkali stress, and to provide a basis for the rational application of silicon fertilizer and efficient N utilization in saline-alkali cotton fields.

Methods A pot experiment was conducted using irrigated gray desert soil and cotton cultivar Xinluzao 66. Five treatments were established: control (CK), alkali stress (AS), alkali stress plus silicon fertilizer (ASSi), salt stress (SS), and salt stress plus silicon fertilizer (SSSi).

Results Compared with CK, AS and SS decreased cotton nitrogen uptake by 27.71% and 26.54%, respectively, and dry matter by 15.09% and 19.13%, while increasing soil NH₄⁺-N by 145.26% and 98.07%, respectively. Compared with AS, ASSi increased cotton nitrogen accumulation by 20.50% and soil NO₃⁻-N by 33.76%, while decreasing NH₄⁺-N by 20.67%. Compared with SS, SSSi increased cotton dry matter and nitrogen accumulation by 12.69% and 22.77%, respectively, decreased NH₄⁺-N by 28.43%, and increased microbial biomass nitrogen (MBN) by 35.32%. Silicon application increased the Shannon index and decreased the Simpson index under both stress conditions. Under alkali stress, silicon application increased the relative abundances of Nitrospira and Nitrosospira and enhanced the modularity of the co-occurrence network of nitrogen-cycling microorganisms; under salt stress, the relative abundance of Nitrosospira increased. Silicon application also altered the relative abundances and taxonomic composition of key nitrogen-cycling functional genes, including amo/pmo, hao, nif, and nir. Under alkali stress, the relative contributions of Nitrospirota to nitrification- and complete nitrification-related functional genes increased by 15.40% and 18.05%, respectively. Under salt stress, the relative contributions of Pseudomonadota to nitrification- and dissimilatory nitrate reduction to ammonium (DNRA)-related functional genes increased by 12.42% and 5.73%, respectively.

Conclusions Saline-alkali stress elevate soil pH, disrupt the equilibrium and diversity of the soil microbial community, and reduce the relative abundance of functional genes associated with ammonia oxidation and nitrite reduction. Silicon fertilization could enhance the structural and functional stability of the microbial community in alkaline soils. Specifically, under alkaline stress, Si application increases the relative abundances of Nitrospira, Nitrosospira, and certain nitrification-related functional genes, while enhancing the relative contribution of Nitrospirota to nitrification- and nitration-related functional genes. Under saline stress, Si application increased the relative abundances of Nitrosospira and certain ammonia oxidation-related functional genes, and elevates the relative contribution of Pseudomonadota to nitrification- and DNRA-related functional genes. Ultimately, Si fertilization increases nitrate nitrogen content and promotes organic nitrogen stability in alkaline soils, enhances microbial biomass nitrogen content under saline stress, and facilitates nitrogen uptake in cotton.