A C-3-symmetric benzotrithiophene tricarbaldehyde (BTT) is synthesized for the first time with a facile method, which is used to construct BTT-based covalent organic frameworks (COFs) with different pore sizes. Meanwhile, the structure transformations of the COFs under high-temperature ionothermal condition are studied systematically, and the relationships between the regularly changed structures of the further-cross-linked COFs and their supercapacitor performances are investigated. It turns out that dealing with COFs of designated structures under ionothermal condition is a great method to build highly conductive structure-controllable materials for electrochemical applications.