Nb-based silicides are promising ultrahigh-temperature materials. However, the structural stability and mechanical properties of Nb-based silicides are markedly influenced by Nb3Si phase. Therefore, the improvement of the stability and mechanical properties of Nb3Si is a great challenge. To solve these key problems, in this work, we apply the first-principles calculations to investigate the influence of transition metals (TM = Mo, Re, Ta, W, Pt, and Ir) on the structural stability, mechanical, and thermodynamic properties of Nb3Si. Two possible doped sites: Nb site and Si site are considered. We find that these alloying elements not only can stabilize the Nb3Si phase but also effectively improve the mechanical properties of Nb3Si. The calculated electronic structure shows that high elastic modulus is attributed to the formation of the TM–Si bond. Importantly, these alloying elements improve the heat capacity of Nb3Si due to the vibration of TM atoms under high temperature. Therefore, our calculated results predict that alloying elements of Re and Ir are beneficial for improving the overall performances of Nb3Si.