Multi-layered design is an effective method to improve the damping performance of structures. The existing research focuses more on the multi-layered design of the structure from the macro-perspective, but lacks attention to the material itself from the micro-perspective. Thus, whether microscale multi-layered (MML) viscoelastic polymers have advantages in damping performance is not clear. Moreover, damping materials preparation and structural noise control is an interdisciplinary study. The noise and vibration control effect of MML viscoelastic polymers in actual composite structures needs to be further investigated. This paper conducts such a study on these issues. First, two different types of MML viscoelastic polymers, i.e., free damping (FD) and micro-constrained damping (MCD) composites, were prepared, and their material properties were characterized. Second, the frequency-dependent damping loss factors and elastic modulus of the different damping composites were identified. The influences of damping composite types and MML designs on material damping loss factor and elastic modulus were compared. Third, a prediction model of vibroacoustic behaviours of the honeycomb sandwich structure was established and validated to investigate the noise and vibration control effects of the MML damping composites on composite structures. The influences of the types, numbers of layers and application positions of the MML damping composites on the honeycomb sandwich structure were studied. The results indicated that MML design is helpful to improve the damping performance of viscoelastic polymers, but its influence on different damping composites is quite different. For noise control, MML-FD is more suitable for controlling airborne sound propagation, while MML-MCD is more suitable for controlling structural sound propagation.