A total of 21 compounds were isolated from the seeds of Capparis masaikai and identified as oxazolidine-2-thione (1), succinimide (2), catechol (3), octathiocane (4), monoethanolamine (5), 3-hydroxypropanenitrile (6), L-arabinose (7), 1,2,3-propanetriol (8), drummondol (9), spionoside B (10), adenosine (11), corchoionoside C (12), coniferin (13), syringin (14), cis-syringin (15), dihydrosyringin (16), indole-3-carboxylic acid (17), β-D-glucopyranosyl indole-3-carboxylic acid (18), 6-hydroxyindole-3-carboxylic acid β-D-glucopyranosyl ester (19), linoleis monoglyceride (20), and triolein (21). Their structures were identified based on physicochemical property and spectroscopic analysis, including MS, NMR, and single-crystal X-ray crystallographic data. Compounds 2–10 and 12–21 were isolated from C. masaikai for the first time.