我們研究在活躍星系中分子雲的物理特性。最近次毫米波陣列望遠鏡(SMA)的觀測發現在一些活躍星系中心區域有一些高溫的分子雲，然而我們對於這些高溫分子雲的加熱機制還尚未清楚。我們透過冷卻(cooling)和加熱(heating)的機制來分析這些高溫分子雲的熱物理性質。在我們的模型中，透過一些原子和分子的冷卻來進行研究，其中包括C I、C II、O I、H2 和CO；並將塵埃、X 射線和宇宙射線視為三種可能的加熱源。由冷卻和加熱的熱平衡，我們發現在這些活躍星系中的冷卻率(cooling rate)高出銀河系的冷卻率約一千倍或更多。而由塵埃及X 射線所造成的加熱並沒有辦法供給所有的冷卻。如果在活躍星系中的冷卻是由宇宙射線來達成熱平衡，由宇宙射線所導致的游離率(ionization rate)高達10 的-13 或-15 次方。研究來自超新星遺骸的宇宙射線發現，這些宇宙射線占所需要宇宙射線的5%不到，無法供給平衡所需要的量。我們認為這麼大量的宇宙射線是來自中心的活躍星系核的活動，如噴流和震波。 We study the physical properties of molecular clouds in active galaxies. Recent SMA observations have discovered several high temperature molecular clouds around the center regions of some active galaxies. The origin of the heating mechanism for these high temperature clouds is unclear. We analyze the thermal properties of these high temperature molecular clouds by considering various cooling and heating mechanisms within these clouds. We consider the cooling of several different atomic and molecular species, including CI, CII, OI, H2, and CO. We consider three heating mechanisms in the active galaxies: dust heating, X-ray heating, and cosmic-ray heating. By considering the thermal balance between cooling and heating, we find that the cooling rates in these active galaxies are about three order or more higher than that in the Milky Way. Our results indicate that the heating from dust grains and X-ray could not account for the total cooling in the active galaxies. If the cooling is balanced by the heating of cosmic rays in the active galaxies, the ionization rates due to the cosmic rays can be as high as 10 to the power of -13 to -15. Studying the cosmic ray from the supernova remnants, we find that these cosmic rays contribute at most 5% of the total cosmic rays and can not account for the amount of cosmic rays required. We suggest that these cosmic rays are from the AGN activities, such as jets or shocks.