A first-principles ab initio density functional and semiempirical molecular dynamics study on the recently discovered low-temperature crystalline to crystalline phase transition of the 1-methyl-3-tetradecylimidazolium hexafluorophosphate ([C(14)mim](+)[PF6](-)) was performed. The results show that the experimentally obtained thermally activated change of the a, b, and c unit cell dimensions basically relates to two different facts. At an increased temperature the longest dimension c is lengthened by increased atomic motions inside the alkyl chain in accordance with the experiments. However, earlier experiments have shown that the dimension a was increased while, curiously, the b dimension was shortened with increasing temperature. Our results show that this unexpected change can be explained by the interconversion of two stable conformations of the [C(14)mim](+)[PF6](-) pair. Related molecular dynamic simulation supports this observation.