During the past decades the tropical Indo-Pacific Ocean has become warmer than before. Meanwhile, both Northern and Southern hemispheric polar vortices (NPV and SPV) exhibit a deepening trend in boreal winter. Although previous studies reveal that the tropical Indian Ocean Warming (IOW) favors intensifying NPV and weakening SPV, how the tropical Pacific Ocean Warming (POW) influences NPV and SPV is unclear. In this study, a comparative analysis is conducted through ensemble atmospheric general circulation model (AGCM) experiments. The results show that, for the northern hemisphere, the two warming exert opposite impacts in boreal winter, in that IOW intensifies NPV while POW weakens NPV. For the southern hemisphere, both IOW and POW warm the southern polar atmosphere and weaken SPV. A diagnostic analysis based on vorticity budget reveals that such an interhemispheric difference in influences from IOW and POW in boreal winter is associated with different roles of transient eddy momentum flux convergence between the hemispheres. Furthermore, this difference may be linked to different strength of stationary wave activity between the hemispheres in boreal winter.