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Supramolecular assemblies of stimuli-responsive amphiphilic molecules have been of utmost interest in targeted drug delivery applications, owing to their capability of sequestering drug molecules in one set of conditions and releasing them in another. To minimize undesired disassembly and stabilize noncovalently encapsulated drug molecules, the strategy of core or shell cross-linking has become a fascinating approach to constructing cross-linked polymeric or small molecule-based nanoassemblies. In this article, we discuss the design and synthetic strategies for cross-linked nanoassemblies from small molecule-based amphiphiles, with robust stability and enhanced drug encapsulation capability. We highlight their potential biomedical applications, particularly in drug or gene delivery, and cell imaging. This feature article offers a comprehensive overview of the recent developments in the application of small molecule-based covalently cross-linked nanocarriers for materials and biomedical applications, which may inspire the use of these materials as a potential drug delivery system for future chemotherapeutic applications. [ABSTRACT FROM AUTHOR]