Shiikuwasha, a citrus fruit native to Okinawa, Japan, has various cultivation lines with distinct free volatile and non-volatile components. However, the glycosylated volatiles, which are sources of hidden aromas, remain unknown. This study aimed to characterize the chemical profiles of free and glycosidically bound volatile as well as non-volatile components in the mature fruits of six Shiikuwasha cultivation lines: Ishikunibu, Izumi kugani-like, Kaachi, Kohama, Nakamoto seedless, and Ogimi kugani. Free volatiles were analyzed using solid-phase microextraction–gas chromatography–mass spectrometry. Glycosides were collected via solid-phase extraction and hydrolyzed with β-glucosidase, and the released volatiles were measured. Additionally, the non-volatile components were determined using non-targeted proton nuclear magnetic resonance analysis. Total free and bound volatiles ranged from 457 to 8401 µg/L and from 104 to 548 µg/L, respectively, and the predominant free volatiles found were limonene, γ-terpinene, and p-cymene. Twenty volatiles were released from glycosides, including predominant 1-hexanol and benzyl alcohol, with Kaachi and Ogimi kugani showing higher concentrations. Principal component analysis (PCA) revealed that taste-related compounds like sucrose, citrate, and malate influenced line differentiation. The PCA of the combined data of free and bound volatile and non-volatile components showed flavor component variances across all lines. These findings provide valuable insights into the chemical profiles of Shiikuwasha fruits for fresh consumption and food and beverage processing.