Shape memory polymers (SMPs) are thermo-rheologically complex materials showing significant temperature and time dependences. Their segments often undergo cooperative phase transitions and conformational relaxations simultaneously along with shape memory effect (SME). In this study, a cooperative domain model is proposed to describe the composition dependence, multiple phase transitions and conformational relaxations of SMPs within their glass transition zones. Variations in local-area compositions and cooperative domains of the amorphous SMPs cause significant differences in their segmental relaxation. At a fixed domain size, both intermolecular activation energy and relaxation time significantly influence the SME and thermomechanical properties of the SMPs. Finally, the model is successfully applied to predict the shape memory behavior of SMPs with one stage SME and triple-SME, and the theoretical results have been validated by the experimental ones. This model could be a powerful tool to understand the working mechanisms and provide a theoretical guidance for the designs of multi-SME in SMPs.