Lotus (Nelumbo spp.) is a valuable plant resource with promising applications in the cosmetic and food industries. To effectively utilize the aromatic compounds of lotus flowers, it is essential to clarify the optimal harvesting organ and flowering stage. In this study, headspace solid-phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC—MS) were employed to investigate the volatile profiles of four lotus cultivars across different flowering stages and floral organs. A total of 63 volatile compounds were identified, including 36 terpenes, 10 benzenoids/phenylpropanoids, and 17 fatty acid derivatives. Among them, 1,4-dimethoxybenzene was the dominant aromatic compound. The volatile profiles of petals differed significantly from those of the other five floral organs. The appendages, a component of the stamens, released the highest concentrations of volatiles, with peak emission at the initial-flowering or full-flowering stages. However, due to pollen dispersal, lotus flowers at full flowering were unsuitable for food or cosmetic applications. Thus, appendages harvested during the initial-flowering stage were the most suitable material for high-quality extraction. This study lays a foundation for the industrial development of lotus flower fragrance.