ABSTRACT Coronal mass ejections (CMEs) erupting from the host star are expected to affect the atmospheric erosion processes of planets. For planets with a magnetosphere, the embedded magnetic field in the CMEs is thought to be the most important parameter to affect planetary mass-loss. In this work, we investigate the effect of different magnetic field structures of stellar CMEs on the atmosphere of a hot Jupiter with a dipolar magnetosphere. We use a time-dependent 3D radiative magnetohydrodynamic (MHD) atmospheric escape model that self-consistently models the outflow from hot Jupiter’s magnetosphere and its interaction with stellar CMEs. For our study, we consider three configurations of magnetic field embedded in CMEs – (a) northward $B_z$ component, (b) southward $B_z$ component, and (c) radial component. We find that both the CMEs with northward $B_z$ and southward $B_z$ increase the planetary mass-loss rate when the CME arrives from the stellar side, with the mass-loss rate remaining higher for the CME with northward $B_z$ until it arrives on the opposite side. The largest magnetopause is found for the CME with a southward $B_z$ component. During the passage of a CME, the planetary magnetosphere goes through three distinct changes – (1) compressed magnetosphere, (2) enlarged magnetosphere, and (3) relaxed magnetosphere for all three CME configurations. The computed synthetic Ly $\alpha$ transit absorption generally increases when the CME is in interaction with the planet for all magnetic configurations but the maximum Ly $\alpha$ absorption is found for the case of radial CME with the most compressed magnetosphere.