Bitumen emulsion has been widely used as the tack coat and surface treatment material for asphalt pavement. A major advantage of this material is it does not require heating during construction. However, it faces the concern of low mechanical strength, especially at high service temperatures. To improve the mechanical strength of bitumen emulsion, various research efforts have been made to use waterborne epoxy resin as a modifier to produce waterborne epoxy modified bitumen emulsion (WEB). To better understand WEB as a paving material, this study aims to investigate the microstructure and evaluate the high-temperature performance and model the creep and recovery behaviour of WEB residues. First, a confocal laser scanning microscopy was employed to investigate the fluorescence microstructure of the WEB residues. The temperature sweep dynamic shear modulus tests were then conducted to characterize the viscoelastic properties of the WEB residues within the temperature range of 4–76 °C, and multiple stress creep recovery (MSCR) tests at 50 °C, 60 °C and 70 °C were conducted to evaluate their high temperature performance. Then, the complex modulus was fitted with Arrhenius model and the activation energy was calculated; and the creep and recovery test results were modelled with both the power law model and generalized Burgers model. Finally, the average percent recovery and non-recoverable compliance were determined. It was found that the rutting resistance of bitumen emulsion can be dramatically increased by incorporating waterborne epoxy resin, and the creep and recovery behaviour of bitumen emulsion can be better fitted by the generalized Burgers model in comparison with the power law model.