In this study, the spoilage potential and molecular mechanisms of a single specific spoilage organism (SSO) Acinetobacter septicus H-MN10 (A. septicus H-MN10) isolated from off-flavoured rice sour soup (RSS) were investigated through the assessment of its metabolic behavior in the fermentation system of RSS. Compared to natural fermentation, the inoculation with this strain significantly altered the physicochemical properties of RSS, including increased viscosity, a darker yellow coloration, elevated pH, decreased levels of amino nitrogen, total acidity, and organic acids. GC-MS analysis identified 168 volatile organic compounds (VOCs). The main off-flavour VOCs included aldehydes (e.g., decanal, nonanal, and 2-octanal), acids (e.g., 2-methylheptanoic acid, acetic acid, and isovaleric acid), and ketones (e.g., 2-octanone, 2-heptanone, and 2-pentadecanone). Transcriptomic analysis further revealed significant changes in gene expression of A. septicus H-MN10 during RSS spoilage and identified the core metabolic pathways and key differentially expressed genes involved in the formation of off-flavour VOCs. This study provided the theoretical basis for understanding food spoilage mechanisms and realizing targeted prevention and control strategies.