We study the phase structure of QCD with three degenerate flavors in the external magnetic fields using highly improved staggered quarks (HISQ). The simulations are performed on $16^3 \times 6$ lattice.In order to investigate the quark mass dependence of the chiral transition we choose the values of the bare quark masses 0.015 and 0.0009375 in the lattice unit, corresponding to $m_\pi=320$ MeV and 80 MeV in the continuum limit. We found no indication of a first order phase transition in the current window of quark masses and external magnetic fields. Unlike to the case with standard staggered fermions inverse magnetic catalysis is always observed at about the critical temperature. The microscopic origin of this phenomena are further discussed by looking into the Dirac eigenvalue spectrum.