Charmonia with different transverse momentum pT usually comes from different mechanisms in the relativistic heavy ion collisions. This work tries to review the theoretical studies on quarkonium evolutions in the deconfined medium produced in p-Pb and Pb-Pb collisions. The charmonia with high pT are mainly from the initial hadronic collisions, and therefore sensitive to the initial energy density of the bulk medium. For those charmonia within 0.1 < pT < 5 GeV/c at the energies of Large Hadron Collisions (LHC), They are mainly produced by the recombination of charm and anticharm quarks in the medium. In the extremely low pT ∼ 1/RA (RA is the nuclear radius), additional contribution from the coherent interactions between electromagnetic fields generated by one nucleus and the target nucleus plays a non-negligible role in the J/ψ production even in semi-central Pb-Pb collisions.