We present a theory for manipulation of d-wave interaction of cold atoms with two lasers strongly driving two photoassociative transitions. The theory predicts the occurrence of a coherence between two excited ro-vibrational bound states due to the photoassociative dipole couplings of ground-state d-wave scattering state to the bound states. We show that this excited-state coherence significantly influences atom-atom interaction. In particular, this leads to the enhancement of d-wave elastic scattering and to the suppression of inelastic scattering. In the presence of an s-wave magnetic Feshbach resonance, the two lasers can couple the s-wave resonance with the d-wave scattering state, leading to the further enhancement in d-wave scattering at relatively low energy. Our numerical calculations based on realistic parameters show that d-wave manipulation would be most effective in case of atoms having excited diatomic states with narrow natural linewidth. We estimate that at an energy of 100 μK the inelastic scattering rate in Yb can be reduced to 20 s −1 while the elastic scattering rate can be two orders of magnitude larger.