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The atomic motions that make up phonons and molecular vibrations in molecular crystals influence their photophysical and electronic properties including polaron formation, carrier mobility, and phase transitions. Discriminating between spectator and driving motions is a significant challenge hindering optimization. Unlocking this information and developing fine-tuned controls over actively participating phonon modes would not only lead to a stronger understanding of photochemistry but also provide a significant new tool in controlling solid-state chemistry. We present a strategy using rationally-designed double pulses to enhance the yield of a photoinduced phase transition in a molecular crystal through coherent control of individual phonons. Using ultrafast spectroscopy, we identified 50 cm-1 and 90 cm-1 phonons responsible for the photoinduced spin-Peierls melting of potassium tetracyanoquinodimethane crystals. We show that the 90 cm-1 phonon can be used to catalyze the phase transition process while the 50 cm-1 phonon enhances the yield of the initial charge transfer reaction.