We present fully atomistic molecular dynamics (MD) simulations at 450 K of two ionic liquid crystals in the smectic phase: 1-dodecyl-3-methylimidazolium tetrafluoroborate ([C12C1im][BF4]) and 1-dodecyl-3-methylimidazolium chloride ([C12C1im]Cl). The two systems experimentally exhibit different ranges of thermal stability of the ionic smectic phase: The chloride salt has a more stable LC phase, between 270.3 K and 377.6 K, with a range of SmA of more than 107 K. In contrast, the tetrafluoroborate salt has a smectic phase between 299.6 K and 311.6 K, with a range of mesophase of just 12 K. The MD simulations show that the chloride system is stable in the smectic phase for the 5 ns of simulation, while the tetrafluoroborate salt melts into an isotropic ionic liquid, in qualitative agreement with the experiments. Comparison of the electrostatic and van der Waals energetic contributions enables one to rationalize the observed behavior as being due to the large size of the [BF4] anion: a larger size of the anion means a lower charge density, and therefore a weaker electrostatic interaction in the ionic layer.