Carbon nanotube (CNT) has fostered research as a promising nanomaterial for a variety of applications due to its exceptional mechanical, optical, and electrical characteristics. The present article proposes a novel and comprehensive micromechanical framework to assess the viscoelastic properties of a multiscale CNT-reinforced two-dimensional (2D) woven hybrid composite. It also focuses on demonstrating the utilisation of the proposed micromechanics in the dynamic analysis of shell structure. First, the detailed constructional attributes of the proposed trans-scale composite material system are described in detail. Then, according to the nature of the constructional feature, mathematical modelling of each constituent phase or building block’s material properties is established to evaluate the homogenised viscoelastic properties of the proposed composite material system. To highlight the novelty of this study, the viscoelastic characteristics of the modified matrix are developed using the micromechanics method of Mori–Tanaka (MT) in combination with the weak viscoelastic interphase (WI) theory. In the entire micromechanical framework, the CNTs are considered to be randomly oriented. The strength of the material (SOM) approach is used to establish mathematical frameworks for the viscoelastic characteristics of yarns, whereas the unit cell method (UCM) is used to determine the viscoelastic properties of the representative unit cell (RUC). Different numerical results have been obtained by varying the CNT composition, interface conditions, agglomeration, carbon fibre volume percentage, excitation frequency, and temperature. The influences of geometrical parameters like yarn thickness, width, and the gap length to yarn width ratio on the viscoelasticity of such composite material systems are also explored. The current study also addresses the issue of resultant anisotropic viscoelastic properties due to the use of dissimilar yarn thickness. The results of this micromechanical analysis provide valuable insights into the viscoelastic properties of the proposed composite material system and suggest its potential applications in vibration damping. To demonstrate the application of developed novel micromechanics in vibration analysis, as one of the main contributions, comprehensive numerical experiments are conducted on a shell panel. The results show a significant reduction in vibration amplitudes compared to traditional composite materials in the frequency response and transient response analyses. To focus on the aspect of micromechanical behaviour on dynamic response and for the purpose of brevity, only linear strain displacement relationships are considered for dynamic analysis. These insights could inform future research and development in the field of composite materials.