Understanding molecular motion in terms of molecular structure is an important issue for microscopic understanding of the nature of transport properties and glass transition, and for design of structured materials to meet specific demands in various applications. Herein, a novel molecular mechanism is proposed to connect macroscopic motion in ionic liquids with molecular structure via conformational conversions of the constituent ions or of the cation-anion pairs. New equations for description of relaxation time, diffusion coefficient, molar conductivity, and viscosity of ionic liquids are established. The equation parameters, which were determined from the temperature dependent heat capacities, self-diffusion coefficients, molar conductivities, and viscosities of typical ionic liquids, were used to produce predictions for the corresponding properties of other ionic liquids and for the glass transition temperatures of representative ionic liquids. All predictions are in nice agreements with the experimental results.