Japonica rice offers high cost-effectiveness and yield, with the potential to replace glutinous rice in Chinese sweet rice wine (CSRW) brewing. It can be classified into aromatic and non-aromatic types, but whether different varieties cause flavor and metabolite differences in CSRW remains unclear. In this study, glutinous rice (GR), three aromatic japonica varieties (CS-217, HXR-450, SXJ-1018), and two non-aromatic varieties (TA-1, HR-1212) were used as raw materials. The qualities of different CSRWs were evaluated through physicochemical indices, sensory evaluation, phenolic and flavonoid contents, antioxidant capacities, HS-GC-IMS, and UPLC-MS/MS. The results showed that CS-217 displayed the highest total acid content, along with excellent overall sensory evaluation, total phenolic content, and antioxidant capacity. A total of 28 VOCs were identified by HS-GC-IMS, among which 13 compounds with VIP ≥ 1, including butyl isobutyrate, butyl acetate, and ethyl pentanoate, were identified as key flavor discriminant factors. Additionally, 2501 non-volatile metabolites were identified, and five key metabolic pathways were revealed. These pathways synergistically regulate CSRW flavor and nutritional quality. Different japonica rice varieties exhibited respective advantages in CSRW quality indicators, providing a basis for the diversification of raw materials in CSRW production.