The long-term degradation behavior of embedded natural fibres is one of the key factors restricting the durability of bio-based mortars and concretes. In this study, to minimize the negative impact of miscanthus fibre on the service life of bio-based miscanthus mortar, the effects of different treatments (heat treatment, milling) on the long-term performance of bio-based miscanthus mortar are investigated. Results show that the heat-treated miscanthus fibres improve the compressive strength and flexural strength of miscanthus mortar by 82.7% and 26.9%, respectively, compared to the reference fibre, thanks to the reduced porosity and enhanced compatibility. The mechanical strength degradation of miscanthus mortar mainly occurs in the first month after being soaked in water. Moreover, the alkaline environment in miscanthus mortar causes the dissolution of some cellulosic components, resulting in the degradation of the miscanthus fibre. The removal of sugar from the miscanthus fibre is conducive to the strength development and durability of bio-based miscanthus mortar. It is concluded that heat-treated miscanthus fibres can be applied to improve the dimensional stability and degradation resistance of miscanthus mortar for better application of miscanthus in sustainable building materials.