Recent insights into covalent organic frameworks (COFs) provide an opportunity for developing new sonosensitizers with the advantages of both small molecules and inorganic nanoagents. Herein, we synthesize two benzotrithiophene-based imine-linked COFs (BTT-DPh-COF and BTT-DPy-COF) through density-functional-theory-guided structure editing. The tailored donor-acceptor (D-A) structures optimize the band position of the COFs and endow them with good intrinsic sonodynamic activity, which can efficiently kill cancer cells, showing excellent sonodynamic therapeutic effect. Particularly, because of the enhanced D-A effect that promotes charge separation and transfer behavior, BTT-DPy-COF exhibits superior ultrasound-triggered reactive oxygen species (ROS) generation capability than BTT-DPh-COF. Therefore, these studies highlight the great potential of elaborate editing COFs with D-A configurations as suitable candidates for advanced sonosensitizers.