Charmonia with different transverse momentum $p_T$ 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 $p_T$ are mainly from the initial hadronic collisions, and therefore sensitive to the initial energy density of the bulk medium. For those charmonia within $0.1<p_T<5$ GeV/c at the energies of Large Hadron Collisions (LHC), They are mainly produced by the recombination of charm and anti-charm quarks in the medium. In the extremely low $p_Tsim 1/R_A$ ($R_A$ 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 $J/psi$ production even in semi-central Pb-Pb collisions.
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