Sigmoidal adsorption in flexible metal-organic frameworks (MOFs) can be achieved through a dramatic phase transition from narrow to large pores; however, such a unique phenomenon, which is not induced by abrupt phase changes, has rarely been reported. We report a series of flexible Hofmann-type MOFs, CoNi-Pipe, NiNi-Pipe, and CoPd-Pipe, pillared with a dimensional (3D) piperazine linker. Owing to the rotational flexibility and 3D dimensionality of the piperazine linker, CoNi-Pipe and CoPd-Pipe exhibited Xe-induced gate opening and the corresponding sigmoidal adsorption isotherms. CoNi-Pipe revealed not only excellent Xe/Kr separation but also Xe recovery performance, attributed to the greatest linker rotation and flexibility, along with moderate Xe binding strength, as validated by the machine learning potential-based molecular dynamics simulations and van der Waals-corrected DFT calculations. Thus, this work provides an effective approach for gaining a deeper understanding of the structural dynamics in flexible frameworks and expanding the repertoire of computational studies.