Vertically aligned carbon nanotube (CNT) arrays are promising candidates for advanced thermal interface materials (TIMs) since they possess high mechanical compliance and high intrinsic thermal conductivity. However, the overall thermal performance of CNT arrays often falls short of expectations when used as TIMs, and the underlying reasons have yet to be fully understood. In this work, the volume fraction of CNT arrays is demonstrated to be the key factor in determining the CNT array thermal transport properties. By increasing the array volume fraction, both the CNT array effective thermal conductivity and the CNT array–glass thermal contact conductance were experimentally found to increase monotonically. One interesting phenomenon is that the increasing rate of thermal conductivity is larger than that of array volume fraction. Compressive experiments verified that the CNT arrays with lower volume fractions suffer from severe buckling, which results in a further decreasing trend. By understanding the underlying reasons behind this trend, the overall thermal performance of vertically aligned CNT arrays can be further increased.