Introduction Soil salinization constrains crop production in arid regions, yet the microbial and functional mechanisms underlying organic-mineral co-application in saline-alkali soils remain unclear.Methods A pot experiment with sorghum-sudangrass was conducted in a saline-alkali soil under five fertilization regimes with equal total N but different proportions of organic N. Soil physicochemical properties were measured at the seedling and maturity stages, and rhizosphere bacterial communities and C, N and P cycling genes at maturity were characterized by 16S rRNA gene sequencing and SmartChip high-throughput qPCR.Results Organic-mineral fertilization decreased soil pH and total salt content and increased soil organic matter, total N and available P relative to mineral fertilizer alone, with the strongest improvements under the 50% organic-50% mineral N regime. Organic inputs increased bacterial Shannon diversity and evenness and shifted community composition, enriching Actinobacteriota, Firmicutes, Bacillus and Pseudarthrobacter. The balanced regime increased genes involved in C degradation/fixation, N fixation and P mineralization/polyphosphate metabolism (e.g., xylA, acsA, mct, nifH, phoD, ppx), whereas mineral-only fertilization favored nitrification/denitrification and methane oxidation genes (e.g., amoA2, nirK, nirS, pmoA), indicating a higher potential for N losses.Discussion Multivariate analyses identified soil pH, total salt, organic matter and total N as primary regulators of bacterial communities and functional gene profiles. Moderate organic-mineral co-application, particularly the 50%-50% regime, improves soil conditions and strengthens nutrient-cycling potential in saline-alkali sorghum-sudangrass systems.