Lotus sprouts are a widely consumed aquatic vegetable, yet their quality remains poorly characterized. This study integrated physicochemical analysis, volatile flavor profiling, and metabolomics to evaluate quality differences among three lotus sprout cultivars, as well as different parts and grades. The apical portions had significantly higher contents of protein, total phenolics, and γ-aminobutyric acid than the stem portions. A total of 46 volatile compounds were identified by headspace solid-phase micro-extraction combined with gas chromatography–mass spectrophotometry (HS-SPME-GC-MS), and the abundance of 2,4-di-tert-butylphenol and 1-octen-3-ol was further confirmed using standards. Untargeted metabolomics identified 335 compounds, with sugars, polyphenols, and amino acids being the most abundant categories. Differentially accumulated metabolites between parts and cultivars were significantly enriched in glutathione metabolism, flavonoid biosynthesis, and amino acid metabolism. Notably, the two Baiyuzan cultivars generally accumulated higher levels of beneficial metabolites than Wuzhi No. 2, whereas the stem portion of the higher-grade Wuzhi No. 2 showed lower accumulation of sucrose and paprazine. Quantitative analysis of eight alkaloids using external standard calibration curves indicated that nuciferine was the most abundant alkaloid (13.3 to 31.1 μg/g). Collectively, this study provides a foundational framework for evaluating the metabolite profiles and application potential of lotus sprouts.