An ultra-thin wearing course is a promising maintenance method for prolonging the service life of the pavement. This study used polyurethane (PU) as a binder to develop an ultra-thin wearing course with high skid and wear resistance (named as PUTWC). The performance and nano-adhesion behavior of PUTWC were investigated by experimental and molecular dynamics (MD) simulation methods. The relationship between the mechanical properties of aggregates and the skid resistance of PUTWC was further analyzed using the grey correlation method. Results indicated that PUTWC using the emery with a particle size of 2–3 mm as the aggregate expressed a more favorable wear and skid resistance, also higher structural stability. The impact and polishing value of aggregates showed a more significant effect on the wear resistance of PUTWC. The adhesive bonding property between the PU and aggregates was investigated using the MD simulation by comparing the interfacial interaction energy, fraction of free volume, and relative concentration distribution of the PU component. Results showed that a stronger adhesion existed between the PU and emery compared with the ceramic particles, which was consistent with the performance test results. The conclusions of MD simulation were confirmed by the test results of scanning electron microscopy (SEM) and positron annihilation lifetime spectroscopy (PALS).