Microscopic information on conformational flexibility and macrocycle-thread binding interactions is helpful in rational design of novel multistation molecular shuttles with interesting topology and functions. Molecular dynamics (MD) was applied to simulate conformational changes of thread and macrocycle of a three-station molecular shuttle in different chemical environments (vacuum, CD3CN-CDCl3 solution, and crystal). In contrast with the highly distorted thread conformation in the gas phase and nonpolar CDCl3 solution, the solvated thread in CD3CN-CDCl3 (1:1) mix solvents exhibited a relatively rigid structure. Experimental observations of preferential binding at the protonated dibenzylammonium group (station I) were rationalized by quantum chemical calculations of macrocycle-thread binding energies at three different stations. The orthogonality of site-specific binding interactions at three different stations was also revealed by the nearly constant binding energy obtained at each specific recognition center with the replacement of different neighboring groups and terminal stoppers on the thread. Conformational flexibility has little effect on NMR signals of binding sites, but for some protons that are close to the solvent molecules in the first solvent shell, their chemical shifts are sensitive to the local electrostatic environment caused by nearby solvents. In crystal, π stacking induced evident upfield shifts of NMR signals in comparison with the isolated monomer.