In the recent times organic semiconductors (OSC) have received attention because of their application in low-cost, flexible, and large area electronics devices. The application of OSC thin films has been limited due to their low charge carrier mobility (~ 0.1 cm²/V_-s). We have investigated the effect of substrate on structure and charge transport characteristics of cobalt phthalocyanine (CoPc) films. Thin films have been grown on both single crystal (sapphire and LaAlO₃) and amorphous (quartz) substrates using molecular beam epitaxy system. The films grown on LaAlO₃ substrates exhibited a higher value of mobility (~ 4 cm²/V-s) while those grown on Al₂O₃ and quartz showed mobility value of ~ 1cm²/V_-s. High mobility for LaAlO₃ substrates has been attributed to the enhanced ordering of the molecules due to natural twin boundaries of substrates. In order to further confirm role of grain boundaries in aligning the CoPc molecules, we measured the charge transport on films deposited at bi-crystal SrTiO₃ substrates. The results showed that current along bi-crystal grain boundary is three orders of magnitude higher than for films on SrTiO₃ substrate without grain boundary, which confirms our hypothesis of ordering of molecules along grain boundaries.