A series of branched ionic liquids (ILs) based on the 1-(iso-alkyl)-3-methylimidazolium cation from 1-(1-methylethyl)-3-methylimidazolium bistriflimide to 1-(5-methylhexyl)-3-methylimidazolium bistriflimide and linear ILs based on the 1-(n-alkyl)-3-imidazolium cation from 1-propyl-3-methylimidazolium bistriflimide to 1-heptyl-3-methylimidazolum bistriflimide were recently synthesized and their physicochemical properties characterized. For the ILs with the same number of carbons in the alkyl chain, the branched IL was found to have the same density but higher viscosity than the linear one. In addition, the branched IL 1-(2-methylpropyl)-3-methylimidazolium bistriflimide ([2mC3C1Im][NTf2]) was found to have an abnormally high viscosity. Motivated by these experimental observations, the same ILs were studied using molecular dynamics (MD) simulations in the current work. The viscosities of each IL was calculated using the equilibrium MD method at 400 K and the non-equilibrium MD method at 298 K. The results agree with the experimental trend. The ion pair (IP) lifetime, spatial distribution function and the associated potential of mean force, cation size and shape, and interaction energy components were calculated from MD simulations. A quantitative correlation between the liquid structure and the viscosity was observed. Analysis shows that the higher viscosities in the branched ILs are due to the relatively more stable packing between the cations and anions indicated by the lower minima in the potential of mean force (PMF) surface. The abnormal viscosity of [2mC3C1Im][NTf2] was found to be the result of the specific side chain length and molecular structure.