Flexible organic crystals enabled by cooperative phase transitions attract enormous interest in solid-state chemistry to produce light, biocompatible, and environmentally benign devices. The recently unveiled super-and ferroelastic organic semiconductor crystals provide a pathway to achieve ultraflexible single-crystal electronics. However, the mechanistic understanding of cooperative transitions in organic crystals is rather at the nascent stage, and most of such studies rely on the trial-anderror approach in molecular design. Compared to the well-studied phase transition in metallic alloys, the key challenge in understanding the organic phase transitions is the elusive crystallography involving intricate molecular dynamics and defects. Here, we leverage the phase transformation theory, genetic algorithm refined molecular modeling, and experimental validation to study the versatile cooperative transitions in bis(triisopropylsilylethynyl)-pentacene semiconductor crystals. The molecular rotation governed thermoelasticity, interconvertible super-and ferroelastic transitions, and molecular twinning are systematically studied by integrating the lattice crystallography and molecular motions. We illustrate the molecular defects of disclination dipoles and molecular stacking faults associated with the molecular twinning process. The fundamental understanding underpins the molecular mechanism of cooperative transitions in a variety of organic solids to promote a new avenue of environmentally responsive organic devices.