The thermal conductivities, thermal diffusivity, thermal anisotropy ratio, and thermal boundary resistance for the multilayered microstructure of a carbon nanotube (CNT) array are reconstructed experimentally using the 3ω method with two different width metal heaters. The thermal impedance in the frequency domain and sensitivity coefficients are introduced to simultaneously determine the multiple thermal parameters. The thermal conductivity at 295 K is 38 W · m−1 · K−1 along the nanotube growth direction, and two orders of magnitude lower in the direction perpendicular to the tubes with the anisotropy ratio as large as 86. Separation of the contact and CNT array resistances is realized through circuit modeling. The measured thermal boundary resistances of the CNT array/Si substrate and insulating diamond film interfaces are 3.1 m2 · K · MW−1 and 18.4 m2 · K · MW−1, respectively. The measured thermal boundary resistance between the heater and diamond film is 0.085 m2 · K · MW−1 using a reference sample without a CNT array. The thermal conductivity for a CNT array already exceeds those of phase-changing thermal interface materials used in microelectronics.