We report on the graphene-assisted growth, crystallization, and phase transition of zinc phthalocyanine (ZnPc) vertically oriented single crystal nanopillars. Postcrystallization thermal annealing of the nanostructures results in a molecular packing change while maintaining the vertical orientation of the single crystals orthogonal to the underlying substrate. Grazing incidence X-ray diffraction and high-resolution TEM studies characterized this phase transition from a metastable crystal phase to the more stable β-phase commonly observed in bulk crystals. These vertical arrays of crystalline nanopillars exhibit a high-surface-to-volume ratio, which is advantageous for applications such as gas sensors. We fabricated chemiresistor sensors with ZnPc nanopillars grown on graphene and demonstrated its selectivity for ammonia vapors, and improvement in sensitivity in the β-phase crystal packing pillars due to their molecular orientation increasing the exposure of the Zn2+ ion to the ammonia analyte. This work highlights the first morphology-retentive phase transition in organic single crystal nanopillars through simple postprocessing thermal annealing. This study opens up the possibility of molecular packing control without large variations in morphology, a necessity for high-performance devices and establishing structure-property relations.