In this paper, we examined the effects of transition metal replacement and ordering in 2D M3C2O2 MXene on the electronic structure and thermal and electrical conductivities using the density functional theory and also Boltzmann’s transport theory within the constant relaxation time approximation. We derived the following oxygen-functionalized ordered double-metal MXenes Ti2YC2O2, Y2TiC2O2, Sc2YC2O2, and Y2ScC2O2 through the surface and sub-layer tuning. The results revealed that the ordered MXenes give rise to different electronic structure and transport properties. The electronic thermal conductivities obtained in terms of the relaxation time increase with increase in absolute temperature, while the electrical conductivities decrease with increase in temperature. The respective transport properties of Y2TiC2O2 and Sc2YC2O2 were found to be enhanced due to the increased squared band velocity, density of state, and low Seebeck coefficient compared to Ti2YC2O2 and Y2ScC2O2 MXenes. Generally, the MXene materials investigated in this work were found to possess metallic properties with the existence of energy overlap around the Fermi level. The computed formation energies support chemical stability in all the materials.