A new heterogeneous catalyst with a unique design was successfully synthesized through a ship‐in‐a‐bottle strategy to incorporate a highly active molybdenum Schiff‐base complex within the nanocages of SBA‐16 for epoxidation reaction. For this aim, all the chemical precursors for preparation of this complex were mixed step by step in the presence of SBA‐16 and the entry of nanocages were finally tuned via silylation with long chain trimethoxyoctylsilane reagent in order to avoid the possible release of encapsulated complex. The final catalyst (named as PPh3‐Sal/Mo@SBA‐16) was characterized by FT‐IR and UV‐Vis spectroscopies, nitrogen adsorption‐desorption and X‐ray diffraction (XRD) analyses as well as scanning and transmission electron microscopies (SEM and TEM). All of these physicochemical techniques approved the incorporation of molybdenum Schiff‐base complex inside the SBA‐16 nanocages and maintenance of physical properties of SBA‐16 after encapsulation process. As predicted, epoxidation of some allylic alcohols and alkenes were proceeded selectively toward desired epoxides with high efficiency beyond 80 % over PPh3‐Sal/Mo@SBA‐16 catalyst. Eventually, the reusability experiment revealed the catalyst stability after five successive epoxidation reaction with only minor reduction of overall efficiency.