Li-ions-intercalated bilayer graphene (BLG) on a SiC substrate can form Kekulé-O mode graphene (Kekulé-O graphene), which has attracted widespread interest for its demonstration of chiral symmetry breaking in particle physics. However, the Kekulé-O mode cannot be observed at high temperatures, which is still a mystery. In this Letter, the effect of the SiC substrate on the migration of Li-ions within the BLG was investigated by first-principles calculations. Our results show that the SiC substrate can significantly reduce the migration energy barrier of Li-ions at both low and high Li concentration. At saturated Li-ion concentration, due to the presence of SiC substrate, Li-ions only need to cross a very small barrier (0.06 eV) to destroy the Kekulé-O graphene. Therefore, the disappearance of Kekulé-O graphene prepared at high temperatures is attributed to the fast migration of Li-ions. This work provides atomic understanding of the temperature modulation of Kekulé-O graphene.