Warm rubberized bitumen (WRB) is a commonly used sustainable material of asphalt pavement in Europe and United States. At present, macroscopic nonlinear rheological properties and microscopic characteristics of WRB samples considering the effect of wax compound structures remain unclear. This paper aims to reveal the potential correlation between the macroscopic non-linear rheological properties and microscopic characteristics of WRB through the combination of rheological tests and microscopic analysis methods. The results show that wax-based additives with higher melting points can crystallize at room temperature to cause the phase separation in WRB system, which can be linked to that nonlinear rheological behaviors of long carbon chain C40 and Sasobit waxes advance the nonlinear stage of the viscosity-temperature curve and reduce linear viscoelastic (LVE) limit compared with short-chain C18 and C24 waxes. The inactivated crumb rubber (CR) has evident phase separation and chemical activation can reduce the average size, area proportion and average number of phase separation due to CR, which can be related to the enhanced nonlinear rheological properties of bitumen after CR addition and deterioration of nonlinear rheological performance of CR after chemical activation. The thermal transition behaviors due to wax crystallization happen at relatively low temperature during the cooling, which can also be associated with more obvious nonlinear performance of WRB sample due to wax crystallization in a low temperature environment. The research results can enhance the understanding of non-linear rheological behaviors and microscopic mechanisms and give guidance for the performance optimization of WRB.