The humid, thermal, and oxidative environments cause the synergistic degradation of asphalt materials. To reveal the long-term ageing mechanism of asphalt in the hygrothermal environments, base asphalt (BA) and styrene-butadiene-styrene (SBS) modified asphalt (SMA) were selected to prepare the short-term, long-term, and hygrothermal-aged samples. Then the changes in micromorphology, molecular weight distribution, chemical compositions, and microstructures of each aged asphalt sample were characterized. The results indicate that the soaking duration is determined as 32 h for preparing the hygrothermal-aged asphalt sample. The moisture diffusion causes physical damage to asphalt, forming circular micro holes on the asphalt surface, which is the main reason to accelerate asphalt ageing. The ambient water and air can easily permeate into asphalt, further accelerating asphalt ageing. Additionally, the small and medium molecular components in the hygrothermal-aged BA are decreased, while the large molecular components become more. Meanwhile, the molecular weight distribution of SMA is relatively concentrated after hygrothermal ageing, and the SBS modifier is degraded from supermolecules to macromolecules. Further, no new chemical compositions are produced after hydrothermal ageing of BA and SMA. The hygrothermal ageing accelerates the oxidation of thioethers and unsaturated carbon bonds to convert into sulfoxide and carbonyl groups. Finally, the hygrothermal ageing destroys asphalt components, and the number of Catana phases on the BA surface is lowered. The Catana phases on the SMA surface were seriously damaged and almost disappeared in asphalt components. The surface elevations of BA and SMA are increased after hygrothermal ageing, but the surface roughness is decreased. This study provides the microscopic insight into the long-term ageing mechanism of asphalt in the hygrothermal environments.