As potential alternatives to inorganic semiconductors for large area, low cost and polymer substrate based devices, organic semiconductors have received much attention during recent twenty years. However, since the structure and performance of vacuum deposited pentacene are very sensitive to numerous deposition parameters, such as pressure, temperature, deposition rate, purity and surface contamination, quite different results have been reported. As a result, many aspects about the growth and charge transport of pentacene film are still not well understood, although a great deal of work has been carried out. In this paper the temperature dependent transport properties were investigated based on the molecular beam deposited pentacene TFTs with both top contact (TC) and bottom contact (BC) structures. The mobility of all devices exhibited Arrhenius relationship with temperature, indicating a thermally activated carrier hopping transport. The mobility also showed strong dependence on the gate field, i.e. increasing the gate voltage would substantially decrease the activation energy Ea derived from the Arrhenius plot. These results were successfully explained by a carrier trap and thermal release transport mechanism. Based on such a mechanism, the density of trap states were evaluated from the temperature and gate dependent mobility. On the other hand, due to the low dispersion van der Waals forces of the organic molecules, obvious structure variation and decreased grain size of the films were observed at a temperature only slightly above room T (45°C). While a phenomenon contradicting the structure variation was that heating resulted in an annealing effect and increased the mobility even after the temperature recovered to room T. Combined with the XRD results, this thermal annealing effect was attributed to the improved structure order in the bottom layers near the film substrate interface. However, the annealing effect was found to be counteracted by the pentacene desorption if higher heating temperatures were used. The results imply that the structure variation should be distinguished when investigating the temperature dependent transport in OFET.