A density functional theory plus Hubbard U method is used to investigate how the incorporation of Pu waste into Gd2Zr2O7 pyrochlore influences its thermo-physical properties. It is found that immobilization of Pu at Gd-site of Gd2Zr2O7 has minor effects on the mechanical and thermal properties, whereas substitution of Pu for Zr-site results in remarkable influences on the structural parameters, elastic moduli, elastic isotropy, Debye temperature and electronic structure. The discrepancy in thermo-physical properties between Gd2−yPuyZr2O7 and Gd2Zr2−yPuyO7 may be a result of their different structural and electronic structures. This study provides a direct insight into the thermo-physical properties of Pu-containing Gd2Zr2O7, which will be important for further investigation of nuclear waste immobilization by pyrochlores.