The organic matter, surface properties and biodegradation of bio-based aggregates are the main factors for their poor performance of bio-based lightweight concrete. In the present study, heat-treatment is applied to bio-aggregates for reducing their negative impacts on cement hydration and performance of thermal insulating bio-based lightweight concrete. The results show that heat-treated bio-aggregates have reduced negative impacts on cement hydration by the decomposition of organic matter and increase of the pH of the leachate, and significantly improves the mechanical strength of concrete. The 28-day compressive strength and flexural strength of heat-treated apricot shell (HAS) concrete increase by 50.2% and 87.7%, respectively, compared to the untreated apricot shell (AS) concrete. The bio-based lightweight concrete in this study has an excellent thermal insulation property, and the thermal conductivity varies from 0.56 W/m·K and 1.25 W/m·K. Moreover, the heat-treated bio-based aggregate significantly reduces the drying shrinkage of concrete. At 108 days, the drying shrinkage of concrete containing heat-treated aggregates reduces by 29.2%-36.1%. Besides, the heat-treated bio-based aggregate enhances the resistance to freeze–thaw cycles, attributed to the reduced micro-cracks and porosity of concrete. Therefore, heat treatment can improve the properties of bio-based aggregates and significantly increase the durability of thermal insulating bio-based lightweight concrete.