Isomeric covalent organic frameworks possessing the same chemical constitutions but different atomic arrangement structures and physicochemical properties are fascinating branches of covalent organic frameworks (COFs). However, the rational design and targeted synthesis of isomeric COFs remain conundrums, so the investigation of isomeric COFs is still in a fledging period. According to the diversity of frameworks, positional isomers with similar structures and framework isomers having distinct constructions are the main existing subspecies of isomeric COFs. In this review, we focus on the research progress and substantial achievements in this fascinating embranchment and systematically summarize and highlight the design principles of both positional isomeric and framework isomeric COFs, which will potentially facilitate further exploitation and investigation of novel isomeric COFs. The application and structure-property relationship of these isomeric COFs have been briefly introduced. Moreover, key constraints of current isomeric COFs and further advancement of this promising field are proposed and anticipated.