Microwave absorption materials in thermal environments should have both high efficiency and high-temperature thermal stability. In this work, carbon nanotubes (CNTs) in-situ grow in the Sc2Si2O7 matrix, which forms three dimensional (3D) networks. These 3D networks have nanometer heterostructure and proper conductivity. The high-temperature microwave absorption properties of CNTs/Sc2Si2O7 ceramics can be optimized by CNTs crystallization with an intermediate conductivity. Particularly, CNTs/Sc2Si2O7 ceramics with annealing temperature (900 °C) have an effective absorption bandwidth (EAB, RC < −10 dB) as wide as 4.2 GHz with the sample thickness from 2.75 mm to 3 mm, and the minimum RC (RCmin) is −47.5 dB with a thickness of 2.75 mm at 673 K. The electronic properties of hetero-interface (CNTs/Sc2Si2O7) are calculated by density function theory (DFT). These electronic properties disclose the displacement of electronics to increase dielectric loss and to improve the microwave absorption properties. Herein, CNTs/Sc2Si2O7 ceramics are promising functional material for the extensive application in high-temperature environments.