The aroma components and sensory characteristics of fresh cheese fermented with three novel probiotics (Lacticaseibacillus rhamnosus B6, Limosilactobacillus fermentum B44, and Lacticaseibacillus rhamnosus KF7) were investigated using an omics approach based on HS-SPME-GC-TOFMS. Multi-dimensional and single-dimensional predictive mathematical models were developed to analyze the relationship between sensory scores and characteristic compounds. The results demonstrated that the three probiotics significantly influenced the volatile metabolite composition and sensory properties of fresh cheese. Totally 16 key aroma compounds (OAV ≥ 1) were identified. Based on OAV and (O) PLS-DA, 4, 7, and 4 significantly upregulated key aroma compounds were detected in the B6, B44, and KF7 groups, respectively. The metabolic pathways of these key compounds were reconstructed, revealing their association with fatty acid β-oxidation, aromatic amino acid metabolism, glycolysis, and esterification. L. fermentum B44, L. rhamnosus KF7, and L. rhamnosus B6 promoted the production of favorable key volatiles, altering flavor profiles. The samples of B6, B44, and KF7 groups exhibited distinct flavor characteristics described as “milk odor”, “cheese odor”, and “lactic odor”, respectively, with the B44 sample achieving the highest overall acceptance. A natural logarithm-based partial least squares regression model was optimized, and the suitability of a nonparametric Bayesian Gaussian regression model for fitting sensory scores was confirmed. Among the identified compounds, 1-pentanol emerged as the most likely sensory score marker. This study elucidated the mechanisms underlying the formation of characteristic flavors and metabolites in probiotic fresh cheese and provided a reliable correlation model to support flavor regulation and quality control.