Molecular reaction coordinates are defined by the interplay of a number of orthogonal nuclear coordinates and are inherently multidimensional for large molecules. Identifying how specific nuclear motions along these reaction coordinates can be used to drive and control chemical processes is a promising approach for the optimization of chemical outcomes and targeted synthetic design. Here, we used femtosecond stimulated Raman spectroscopy (FSRS) to quantify the effects of individual phonon nuclear motions on singlet fission in rubrene derivatives. Rubrene readily undergoes singlet fission and is amendable to chemical derivatization, yet the factors that impact the singlet fission yield are not fully understood. Crystal packing is known to play a significant role in both fission and carrier transport, and thus, we focused on the impact of phonon nuclear motions on the photophysics. We used four halogen-substituted rubrene crystals and successfully identified one specific phonon mode that suppresses singlet fission in these crystals. We used FSRS with single-pulse excitation and double-pulse excitation to coherently amplify each phonon mode and quantify its effects on the excited-state process. We found that coherent amplification of the specific phonon vibration involving twisting of the peripheral phenyl rings and tetracene core motions resulted in less ground-state depletion and fewer triplet state absorption. Our study demonstrated that it is possible to use coherent phonon excitation to influence the photophysical outcome, while also showing that FSRS with double-pulse excitation can be a successful tool for quantifying mode-selective contributions to photophysics.