As a bitumen modifier, waste thermoplastic polyurethane (TPU) could effectively improve the intermediate and low temperature pavement performance of bitumen and increase the recycling rate of waste. However, the high temperature performance of TPU modified bitumen is insufficient, which limits the application of TPU modified bitumen in pavement engineering. The objective of this study is to improve the high temperature performance of TPU-modified bitumen by compounding amorphous poly alpha olefin (APAO). The orthogonal test of TPU/APAO modified bitumen was conducted to determine the preparation process parameters. The physical and rheological properties of TPU/APAO modified bitumen were investigated by penetration, softening point, ductility, elastic recovery, viscosity, dynamic shear rheometer (DSR, including temperature sweep and multiple stress creep recovery), and bending beam rheometer (BBR) tests. The compatibility and modification mechanism of TPU/APAO modified bitumen were studied by storage stability, fluorescence microscopy (FM), and Fourier transform infrared spectroscopy (FTIR) tests. The test results show that the optimum preparation process of TPU/APAO compound modified bitumen is 5000 rpm for 60 min at 190 °C. The addition of APAO reduces penetration and ductility, increases softening point and viscosity of TPU modified bitumen. The low temperature performance is not sacrificed with the improvement of the high temperature PG grade. Besides, the anti-aging properties and creep recovery rate of compound modified bitumen are optimal at 2% TPU and 6% APAO. The proper content of APAO can improve the compatibility between TPU and bitumen. APAO is physically mixed with bitumen, but the free isocyanate in TPU can react with the polar carboxyl group (asphaltene) and their product is closely related to the PU bond.