The stabilization energies (E(form)) for the formation of the perfluoroalkyltrifluoroborate complexes with Li(+) and 1-ethyl-3-methylimidazolium cation (emim(+)) were calculated at the MP2/6-311G** level. The E(form) values calculated for the Li[BF(4)], Li[BF(3)CF(3)], Li[BF(3)C(2)F(5)], Li[BF(3)C(3)F(7)], and Li[BF(3)C(4)F(9)] complexes were -144.1, -139.3, -137.4, -136.3, and -135.4 kcal/mol, respectively. The E(form) values calculated for the [emim][BF(4)], [emim][BF(3)CF(3)], [emim][BF(3)C(2)F(5)], [emim][BF(3)C(3)F(7)], and [emim][BF(3)C(4)F(9)] complexes were -85.2, -81.2, -79.7, -79.7, and -79.2 kcal/mol, respectively. The electrostatic interactions are the major source of the attraction in the complexes, whereas the contribution of the induction interactions to the attraction is not negligible. The interactions of the perfluoroalkyltrifluoroborate anions with Li(+) and emim(+) are substantially weaker than those of the BF(4)(-) because of the weaker electrostatic interactions. The analysis of the interactions suggests that the weaker interactions between the BF(3)CF(3)(-) and emim(+) compared with those between the BF(4)(-) and emim(+) are the cause of the lower viscosity of the [emim][BF(3)CF(3)] ionic liquid compared with the [emim][BF(4)] ionic liquid. The order of experimental self-diffusion coefficients of the cations and anions in the ionic liquids is BF(4)(-) < BF(3)CF(3)(-) approximately BF(3)C(2)F(5)(-) > BF(3)C(3)F(7)(-) > BF(3)C(4)F(9)(-), which is well reproduced by the molecular dynamic simulations. The analysis of the rotational relaxation of emim(+) suggests that the translational diffusion of cations and anions is associated with the rotational diffusion of emim(+).