The most precise to-date evaluation of the nuclear recoil effect on the $n=1$ and $n=2$ energy levels of He-like ions is presented in the range $Z=12-100$. The one-electron recoil contribution is calculated within the framework of the rigorous QED approach to first order in the electron-to-nucleus mass ratio $m/M$ and to all orders in the parameter $alpha Z$. The two-electron $m/M$ recoil term is calculated employing the $1/Z$ perturbation theory. The recoil contribution of the zeroth order in $1/Z$ is evaluated to all orders in $alpha Z$, while the $1/Z$ term is calculated using the Breit approximation. The recoil corrections of the second and higher orders in $1/Z$ are taken into account within the nonrelativistic approach. The obtained results are compared with the previous evaluation of this effect [A. N. Artemyev et al., Phys. Rev. A 71, 062104 (2005)].