Femtosecond vibrational spectroscopy was used to measure the vibrational population relaxation time ($T_1$) of different anions bound to ferric myoglobin ($Mb^{III}$) and hemoglobin ($Hb_{III}$) in $D_2O$ at 293 K. The $T_1$ values of the anti-symmetric stretching (${ u}_1$) mode of NCS in the $NCS^-$ bound to $Mb^{III}$ ($Mb^{III}$NCS) and $Hb_{III}$ ($Hb_{III}$NCS) in $D_2O$ are $7.2{pm}0.2$ and $6.6{pm}0.2$ ps, respectively, which are smaller than that of free NCS. in $D_2O$ (18.3 ps). The $T_1$ values of the ${ u}_1$ mode of NCO in the $NCO^-$ bound to $Mb^{III}$ ($Mb^{III}$NCO) and $Hb_{III}$ ($Hb_{III}$NCO) in $D_2O$ are $2.4{pm}0.2$ and $2.6{pm}0.2$ ps, respectively, which are larger than that of free $NCO^-$ in $D_2O$ ($1.9{pm}0.2$ ps). The smaller $T_1$ values of the ${ u}_1$ mode of the heme-bound NCS suggest that intramolecular vibrational relaxation (VR) is the dominant relaxation pathway for the excess vibrational energy. On the other hand, the longer $T_1$ values of the ${ u}_1$ mode of the heme-bound NCO suggest that intermolecular VR is the dominant relaxation pathway for the excess vibrational energy in the ${ u}_1$ mode of $NCO^-$ in $D_2O$, and that intramolecular VR becomes more important in the vibrational energy dissipation of the ${ u}_1$ mode of NCO in $Mb^{III}$NCO and $Hb_{III}$NCO.