In the upgrades and innovations of nuclear fuel material, the U-50 wt.% Zr alloy is regarded as one of the most promising metallic fuel materials, due to its excellent thermal response, acceptable irradiation performance, and ease of fuel recycling. Under in-pile irradiation, large temperature gradients and dimensional changes contribute to complicated fuel thermal-mechanical behaviors, including the pore effect induced by fission gas production. However, the deficiency of the physical parameters of the porous U-50 wt.% Zr alloy makes it hardly possible to conduct fuel performance prediction under high irradiation conditions. To obtain Young’s modulus and thermal conductivity of porous U-50 wt.% Zr alloy, the molecular dynamics (MD) code LAMMPS and the modified embedded atom method (MEAM) potential for binary U-Zr system were incorporated. In this study, three-dimensional elastic constants were calculated by engineering strain loading method at different ambient temperatures and porosities, and the effective Young’s modulus was computed via Voigt averaging scheme. The phonon thermal conductivity was simulated with the Non-Equilibrium Molecular Dynamics (NEMD) method, and the electron thermal conductivity was predicted by semi-empirical correlations and existing density functional theory (DFT) results. The parallel model, series model and effective medium theory (EMT) were adopted to consider the mixture and pores effect. Finally, porosity factors were proposed to establish new semi-empirical correlations, which could give a preliminary prediction of Young’s modulus and thermal conductivity for porous U-50 wt.% Zr alloy.