To address issues of water resource waste, nutrient loss, and unstable natural fermentation flavor in traditional high-salt fermented chili, this study isolated and screened aroma-enhancing functional bacteria from 8% low-salt chili fermented naturally at room temperature, and further investigated their application in low-salt chili fermentation. Using the gradient dilution and spread plate method, 11 lactic acid bacteria (R1-R11) and 7 yeast strains (J1-J7) were isolated. Based on colony morphology, physiological and biochemical characteristics (acid production and antibacterial activity of lactic acid bacteria, gas production, film formation, and acid tolerance of yeasts), 3 superior lactic acid bacteria (R3, R4, R5) and one yeast strain (J1) were selected. Control groups included room-temperature natural fermentation (CK1), uninoculated fermentation at 32 °C (CK2), and a commercial 18% high-salt desalted seasoning product (CK3). The selected strains were applied in single-strain fermentations at 32 °C under low-salt conditions, and the aroma and quality of chili fermented for 15 days were analyzed. Molecular identification confirmed that strain R3 was Lactiplantibacillus plantarum and J1 was Meyerozyma guilliermondii. In the volatile compound analysis, the R3 group produced 76 volatile organic compounds (VOCs) with 14 key aroma compounds (relative odor activity value, rOAV ≥1), more than CK1 (11), CK2 (13), and CK3 (10). Characteristic aroma compounds such as d-limonene, geranylacetone, and hexanal were significantly enriched, with acids (32.37%) and esters (22.09%) contributing prominently. The J1 group yielded 74 VOCs with 14 key aroma compounds, where esters accounted for 36.91%, higher than CK1 (16.29%), CK2 (18.10%), and CK3 (33.46%). Unique aroma compounds such as 1-nonanol, benzyl alcohol, and linalool were notable. Sensory evaluation indicated that the R3 group achieved aroma scores second only to CK3, while the J1 group received positive feedback for its ester-rich aroma. By contrast, CK1 and CK2 showed inferior aroma quality, with CK1 containing minor undesirable capric acid and CK2 producing off-flavor 3-methylbutanoic acid, and both groups dominated by alkanes (30.97% and 31.72%, respectively), which contributed little to aroma. Overall, R3 (L. plantarum) and J1(M. guilliermondii) significantly enhanced the aroma complexity and quality of low-salt chili fermentation. These strains hold potential as functional starter cultures for low-salt chili fermentation, providing both theoretical support and microbial resources to promote industrial-scale production.