To address the unclear microbial community structure and lack of efficient fermentation strain combinations in Ningxia traditional sourdough, this study employed metagenomic sequencing to dissect its microbiota composition, coupled with conventional isolation and functional screening to obtain candidate strains with desirable fermentation properties and evaluate their combinatorial fermentation efficacy. The results revealed that the sourdough microbiota was dominated by lactic acid bacteria and yeasts as core functional groups. The bacterial community exhibited significant compositional variation, with predominant species including?Fructilactobacillus sanfranciscensis?(24.54%),?Pediococcus acidilactici?(15.99%),?Pediococcus pentosaceus?(8.20%), and?Leuconostoc mesenteroides?(7.69%). The fungal community structure was relatively concentrated, predominantly dominated by?Saccharomyces cerevisiae?(90.99%), with only individual samples (e.g., LM2) being primarily composed of?Candida zeylanoides?(73.73%). Based on isolation, cultivation, and functional evaluation, ten lactic acid bacterial strains with strong acid-producing capacity and eleven yeast strains with superior gas-producing performance were obtained. Further screening identified candidate fermentation strains including?Lactiplantibacillus plantarum?M6-1,?Pediococcus acidilactici?M10-1,?Pichia kudriavzevii?Y1-1,?Saccharomyces cerevisiae?Y6-2, and?Saccharomyces boulardii?Y10-2. Co-fermentation experiments demonstrated that the four-strain combination (M6-1, M10-1, Y6-2, Y10-2) exhibited superior dough fermentation performance, with the highest total free amino acid content in fermented dough reaching 1253.24 mg/kg. This combination partially aligned with the natural dominant microbiota structure of traditional sourdough, not only corroborating the synergistic interaction between lactic acid bacteria and yeasts and the pivotal role of core functional microbiota, but also providing microbial resources and theoretical foundations for the development of composite starter cultures in traditional cereal-based products.