The molecular orientation and order in the initial growth of copper phthalocyanine on Si(111) was investigatedin situ by angular-dependent X-ray absorption spectroscopy. A transition from lying-down to standing-upconfiguration occurs in less than one monolayer. After the Si surface is passivated by a monolayer of themolecules, only the standing-up structure persists in subsequent growth. The molecular film also exhibits anorder-disorder-order transition in the distribution of molecular tilt angle during growth. These transitionsare related to the changes of interactions in the system at different stages.