This study offers a comparative evaluation of freeze-drying (FD), hot-air drying (HD), and traditional sun drying (SD) on the physicochemical properties of Hemerocallis citrina Baroni cultivars, aiming to address a critical gap in postharvest processing optimization. By systematically assessing multiple quality parameters—nutritional composition, bioactive compound retention, antioxidant capacity, and flavor profiles—this work highlights the distinct benefits of each drying technique. FD preserved thermolabile compounds most effectively across both cultivars, maintaining significantly higher levels of essential nutrients (total sugars, soluble proteins, ascorbic acid) and bioactive compounds. In MLHH, FD retained superior levels of polyphenols (5.58 mg/g), flavonoids (1.72 mg/g), and carotenoids (54.70 μg/g) compared to HD (4.80, 1.28, 11.62 mg/g) and SD (3.10, 0.49, 7.45 mg/g). XHH showed even higher retention under FD for these compounds, with polyphenols reaching 7.15 mg/g and flavonoids at 2.37 mg/g. These enhanced bioactive contents corresponded to superior antioxidant activity, particularly in XHH where FD achieved 84.60% ABTS radical scavenging compared to HD (43.18%) and SD (76.44%). While SD demonstrated superior flavor development, yielding the highest volatile compound content in XHH (69.01 mg/kg vs. FD: 16.02, HD: 15.84 mg/kg), HD showed selective advantages in mineral retention, particularly for calcium in MLHH (HD: 4025 mg/g, FD: 3537 mg/g, SD: 3225 mg/g). This comprehensive analysis thus establishes evidence-based guidelines for tailoring drying protocols according to specific quality requirements, facilitating targeted approaches in functional food development and nutraceutical manufacturing.