BiCuSeO has recently been shown to be one of the best oxide-based thermoelectric materials. The electrical properties of this material have been widely studied; however, the reasons for its intrinsically low thermal conductivity have only been briefly discussed. In this paper, we calculated the band structure and the electrical properties of BiCuSeO. The phonon spectrum, mode Grüneisen parameters and the thermal properties were also investigated. Additionally, we proposed a new method for illustrating the interlayer interactions in this material. For the first time, using first principles calculations, we provide direct evidence of the structural in-layer and interlayer off-phase vibration modes, which contribute to the anharmonic vibrations and structural scattering of phonons and result in an intrinsic low lattice thermal conductivity for BiCuSeO.