Abstract:[Background] The extreme environments of Qinghai-Xizang Plateau harbor unique microbial resources with special biological activities. [Objective] To investigate the maize (Zea mays) growth-promoting effect of Bacillus atrophaeus NLHLT2 isolated from Qinghai-Xizang Plateau. [Methods] We employed bioactivity assays, whole-genome sequencing, and gene function analysis to characterize the bioactivity and related functional genes of the strain. The bacterial suspension with a concentration of 2×108 CFU/mL was prepared and diluted in gradients of 100, 150, 200, 250, and 300 folds, and the optimal concentration for promoting plant growth was determined. Under low-temperature conditions, maize seedlings were treated with the strain suspension at the optimal concentration via root irrigation, and the effect of the suspension on maize growth was evaluated. [Results] Strain NLHLT2 exhibited significant antagonistic activities against plant pathogenic fungi Fusarium graminearum and Nigrospora oryzae. Meanwhile, the strain possessed the abilities to produce siderophores, gibberellins, and cytokinins and both salt and low-temperature tolerance. Under low-temperature conditions, root irrigation with the strain suspension (1×106 CFU/mL) significantly enhanced the plant height, root length, leaf area, biomass, superoxide dismutase activity, peroxidase activity, and proline content, while markedly reducing the malondialdehyde content in maize seedlings. These effects collectively improved the physiological adaptability of maize seedlings to low-temperature stress. The complete genome sequence of strain NLHLT2 was 4 212 529 bp, with the G+C content of 43.29%. The genome contained functional genes associated with plant growth promotion and stress responses. [Conclusion] By studying the biological activity and genomic characteristics of strain NLHLT2, we analyze the genes related to growth promotion and stress tolerance, aiming to reveal the interaction mechanism between the strain and maize under low-temperature conditions. This study provides an elite strain and a theoretical basis for maize growth in high-altitude regions.