Polyurethane (PU) can be used as a road material binder, and its mechanical properties, durability, temperature stability, and other road performance metrics are good. However, the interlayer bonding between PU mixtures and asphalt mixtures is poor. The influence of the pavement structure, interlayer treatment scheme, load, and environmental factors on the interlayer shear characteristics of PU mixture composite pavement is analysed. Further, dynamic modulus, Hamburg rutting, accelerated loading, and inclined shear tests were conducted, and the typical PU mixture pavement shear stress was calculated. The interlaminar shear stress of double layer PU mixture pavement, polyurethane–asphalt composite pavement, and typical asphalt pavement were calculated. The results showed that the PU mixture has a low rutting deformation rate, stable mechanical properties, and strong resistance to the coupled action of temperature, water, and loading. The double-layer PU mixture structure has good water-temperature stability and fatigue resistance; however, freeze–thaw and accelerated loading cause great damage to the double-layer PU mixture structure. The residual shear strength ratio after freeze–thaw cycles and accelerated loading is only 50.3% and 35.6%, respectively, while the influence on the double-layer asphalt mixture structure is less. The theoretical calculation results of different pavement structures show that when the temperature increases from 10 °C to 50 °C, the interlaminar shear stress of polyurethane–asphalt composite pavement increases by about 20%. Additionally, the shear stress of pavement PU mixture pavement and typical asphalt pavement is mainly affected by load, and the temperature changes have an obvious effect on the interlayer shear stress of polyurethane–asphalt composite pavement. The calculated maximum shear stress of the three pavement structures with different working conditions is less than the interlaminar shear strength measured by the inclined shear test, indicating that the interlaminar treatment scheme of composite specimens can meet the shear resistance requirements of the three typical pavement structure types.