Microwave heating (MH) as a sustainable pavement maintenance method can effectively repair the cracks caused by freeze-thaw (FT) damage. However, binders' properties may be weakened during this process then reduces the pavement life. For this purpose, this work aims to investigate the performance changes of neat binders (Nb) and high-viscous binders (Hb) during FT and MH. The physicochemical, rheological, and deformation properties are investigated after FT and MH. Results indicate that asphalt binders become harder and lead to an increase in carbonyl index (CI) and sulfoxide index (SI) after FT. MH has a limited damage level for binders especially for Hb, causing a slight increase in CI and SI, compared to binders after FT. Polymers play an important role in the viscoelastic responses of asphalt binders. Changes in viscoelastic properties of Nb mainly result from the binder damage of FT and MH, while viscoelastic changes of Hb are mainly due to the damage of polymers. This different damage mechanism causes Hb to show better resistance compared to Nb, which is reflected in modulus and phase angle. BBR tests indicate that MH can further deteriorate the damage of both binders, but Hb shows a lower performance decline compared to Nb, and it is recommended to conduct MH at the region with a minimum temperature above −12 °C. MSCR results reveal that FT and MH can improve the rutting resistance of Nb due to the hardening phenomenon after damage, and reduce the elastic stability of Hb due to the damage to polymers. In summary, Nb is sensitive to MH, its performance can be further damaged after MH. Hb has better resistance to MH, its properties do not further deteriorate, so Hb is more applicable to MH.