Four onion (Allium cepa L.) cultivars with different bulb colors (yellow Y14, red R12, red R10 and white W3) were characterized for phenotypic, metabolic, volatile, antioxidant, flavor and transcriptomic variations, to unravel key metabolites and molecular mechanisms responsible for quality differentiation. Y14 possessed the maximum bulb weight (535.34 g) and diameter (13.10 cm), along with the highest total phenolic content (3.10 mg·g⁻¹), showing superior yield and antioxidant properties. In R12, upregulated expression of carotenoid biosynthetic genes enhanced carotenoid accumulation, resulting in vivid bulb color. R10 had high total phenols (3.89 mg·g⁻¹) and the richest sweet-associated volatiles, featuring strong antioxidant activity and distinct sweetness. By contrast, W3 exhibited moderate flavor but inferior performance in yield, antioxidant capacity, pigment and volatile levels relative to the other three cultivars. Comprehensive assessment indicated that Y14 serves as an excellent processing material, R12 and R10 are ideal for fresh consumption and functional food development, and W3 is well-suited for raw salads. This study lays a theoretical foundation for onion quality improvement, targeted breeding and efficient utilization.