Candida antarctica lipase B-catalyzed glycerolysis of sunflower oil in a tetraammonium-based ionic liquid (IL) was studied to elucidate its distinct characteristics and to evaluate the contributions of important parameters. Mass transfer limitations and occurring partial phase separation were found to have a profound effect on the lower initial rate and the occurrence of the induction period. The investigation on the rheological behavior of the IL and its mixture with substrates showed that the plot of the viscosity of pure IL against temperature was better fitted with the Vogel–Tammann–Fulcher (VTF) equation, and the viscosity of the mixture is strongly agitation-dependent. A comparable diffusion time constant of the oil molecule in the IL to that of the reaction shows that the glycerolysis in the IL is controlled both diffusionally and kinetically, as experimentally verified by agitation effect and enzyme loading study. Interestingly, increasing water activity resulted in a decreasing initial reaction rate and a prolonged induction period, which possibly resulted from an elevated solvation barrier and the phase separation at higher water content. Studies on thermodynamics of glycerolysis show that there is a bigger energy barrier for the IL system, about 1.5 times that of the solvent-free or 3 times that of the tert-butyl alcohol system. Kinetic studies also show that IL system has the biggest Vmax and Km among the three tested systems, indicating, respectively, its high productivity, and low substrate affinity to enzyme due to mass transfer limitation.