A two-level atom passing through double spatially separated single-mode cavity fields is studied. We investigate the effecting factors of photon emission probabilities of the atom, which include the kinetic energy of the atom, the length of the cavity and the separation between the two cavities. The results show that in the case of ultra-cold atom, when the kinetic energy of the atom is small (k/k0k/k0>1), the length of the cavity has great effect on the photon emission probabilities. The present work shows that the photon emission probabilities may be modulated by controlling the center-of-mass motion of the atom.