[Objective] To provide environmental sustainable, safe, and efficacious management approaches for root rot impacting a range of crops in the unique agro-ecosystems of Gansu and Qinghai Provinces. [Methods] The plate confrontation method and the organophosphorus agar plate were used for preliminary screening of 305 strains of tested bacteria, and the strains obtained from preliminary screening were re-screened with the fermentation broth method. Subsequently, the nitrogen-fixing, phosphate-solubilizing, and potassium-solubilizing abilities of the strains were determined by the Kjeldahl method, ultraviolet spectrophotometry, and flame photometry, respectively. The siderophore-producing activity, the IAA content in the fermentation broth, as well as the acid, alkali, and salt tolerance of the strains, were determined by spectrophotometric methods. Finally, targeting the pathogens causing root rot in various crops in Gansu and Qinghai Provinces, bacterial consortia were constructed with different functional strains for disease prevention and plant growth promotion. The plant growth-promoting and antifungal effects of different consortia were evaluated, and the best consortium was selected. Furthermore, the 16S rRNA gene and gyrB of the strains in the best consortia were sequenced for identification. The root rot-preventing and plant growth-promoting effects of the best consortium were evaluated by the pot culture method. [Results] A total of 86 antagonistic strains and 134 phosphate-solubilizing strains were preliminarily screened out, and 20 antagonistic strains were selected after re-screening, among which strains K87 and LB17 demonstrated excellent broad-spectrum antifungal effects. Specifically, K87 showed inhibition rates of 87.53%, 74.90%, 75.15%, 79.69%, and 88.43% against Fusarium avenaceum, F. equiseti, F. oxysporum, F. solani, and Microdochium bolleyi, respectively. LB17 exhibited inhibition rates of 61.89%, 87.52%, and 87.23% against F. oxysporum, F. solani, and Bipolaris sorokiniana, respectively. Among the 8 strains with superior plant growth-promoting abilities, LB17 had the strongest siderophore-producing activity, with an iron carrier activity unit (su) value of 0.32, and K113 exhibited a good nitrogen-fixing capability, fixing nitrogen at a rate of 0.08 g/L. K87 secreted the highest amount of IAA, which reached 9.87 mg/L. MP6 had the greatest ability to solubilize inorganic phosphorus, with a solubilization rate of 1 470.69 μg/mL, while K85 showed the best performance in solubilizing organic phosphorus, with a solubilization rate of 1 321.23 μg/mL. MP41 excelled in potassium solubilization, with a solubilization rate of 140.33 mg/L. Ultimately, 14 bacterial consortia were constructed, in which T2 exhibited the best synthetic performance, with a nitrogen-fixing rate of 0.212 g/L, a potassium solubilization rate of 86.28 mg/L, and an IAA secretion rate of 16.91 mg/L. Moreover, its inhibition rates against the 6 pathogenic fungi all reached over 60.00%, and even 87.69% against F. equiseti. Strains LB17, K87, and MP6 in this consortium were all identified as Bacillus velezensis. T2 demonstrated significant biocontrol efficacy against root rot in naked barley, with the control effects exceeding 70.00%, and exhibited remarkable plant growth-promoting properties. [Conclusion] This study developed an efficient bacterial consortium for the management of crop root rot and the promotion of crop growth in the unique agro-ecosystems in Gansu and Qinghai Provinces.