In this letter a beat phenomenon is reported in molecular dynamics simulations for vibrating boron nitride-carbon nanotubes (BN-CNTs) and then analysed based on a continuum mechanics theory. It was shown that the distinctive dynamic behaviour is a result of the superposition of two orthogonal transverse vibrations whose frequencies are slightly different due to the oval cross-section of the hybrid nanotubes. In particular, the interaction between the two vibrations in BN-CNTs will facilitate to resolve the fundamental issue in developing mass nanosensors for atomic-scale mass measuring. To reach this goal, efforts should be made to maintain high quality factor of the BN-CNT oscillating system by minimising the damping effect of its surrounding environment. This issue turns out to be essential for the beat mode-based nanosensors as large damping will reduce the hybrid nanotubes to conventional resonators with *