The selective separation of structurally similar aliphatic/aromatic hydrocarbons is an essential goal in industrial processes. In this study, we report the synthesis of a water-soluble (Tr 2 M 3 ) 4 L 4 (Tr = cycloheptatrienyl ring; M = metal; L = organosulfur ligand) molecular cage (1) via self-assembly of the water-soluble acceptor tripalladium sandwich species [(Tr 2 Pd 3 )-(CH 3 CN)][NO 3 ] 2 and the attachment onto L of solubilizing methoxyethoxy appendants to be utilized in an energy-friendly alternative approach to the separation of structurally similar molecules under ambient conditions. Cage 1, comprising a hydrophobic inner cavity, exhibited good solubility and stability in aqueous media. It also demonstrated excellent performance in the sequential separation of alkanes (C6−C9), xylene, and other disubstituted benzene isomers and cis/trans-decalin.