In this paper, we present a simple scheme for efficiently removing the residual Doppler background of a comb laser based two-photon spectrometer to be better than 10−3 background-to-signal ratio. We applied this scheme to stabilize the frequencies of a mode-locked Ti:sapphire laser directly referring to the cesium 6S–8S transition and rubidium 5S–5D transition. We suggest a standard operation procedure (SOP) for the fully direct comb laser stabilization and evaluate the frequency of two spectral lines at a certain temperature, by which we demonstrate an all-atomic-transition-based Ti:sapphire comb laser merely via a 6-cm glass cell.