We study the thermodynamics of QCD system under external magnetic field via the 2+1 flavor Polyakov-loop quark-meson model. To incorporate quantum and thermal fluctuations, the functional renormalization group approach is implemented in our work. Pressure, entropy density, magnetic susceptibility and other thermodynamic quantities are calculated and analyzed to investigate the effect of magnetic field on the QCD system. The calculated results are in reasonable agreement with lattice QCD simulations and perturbation theory. We then give an intuitive picture for the response of QCD system to the magnetic field.