The Y‐organs (YOs) synthesize and secrete molting hormones, and thus regulate crustacean growth and reproduction. However, the YOs of the orange mud crab Scylla olivacea is yet to be described due to its minute size and ambiguous feature. This study describes the location, morphological characteristics, histology, and the changes of YOs at different molt stages, and examines in vitro ecdysteroid secreted by the YOs of S. olivacea. Mature male crabs (> 90 mm carapace width, CW) were used to identify the location of the YOs while male juveniles (50–65 mm CW) at three molt stages (intermoult, premoult, postmoult) were dissected for the characterization of 20‐Hydroxyecdysone (20E) levels. The yellowish‐white, compact, and oval‐shaped YOs are located in pairs at the anterior cephalothorax region, beneath the mandibular external adductor muscle, anterior to the branchial chamber space, and around the end of the nerve tract. The YOs index and YO's cell diameter increased from postmoult to premoult; YO's diameter increased only during premoult stage. Under electron microscopy, the YO's surface morphology is rough, bumpy, network‐like, and porous, with several lacunar system tubules. High concentrations of haemolymph 20E during premoult correlated with the changes in the characteristics of YOs at this stage. The presence of ecdysteroid in YOs was confirmed by high performance liquid chromatography (HPLC). The characteristics of the YOs of S. olivacea are similar to the YO descriptions of other brachyurans. The successful identification and characterization of YOs will spearhead future research on understanding its role in molt regulation of mud crabs, consequently contributing to the development and progress of crab culture and soft‐shell crab industries.