A bolaamphiphilic cross-linked nanoassembly endowed with pH responsive degradation features has been designed and fabricated for stable noncovalent guest encapsulation and controlled release. The self-assembled bolaamphiphile is utilized to prepare cross-linked nanoassemblies to further stabilize the noncovalent guest encapsulation at a concentration below its critical aggregation concentration (CAC) in a large volume of water or serum for drug delivery applications. Thus, this system can simultaneously address premature drug release and safety issues. The nanoassemblies integrated with a β-thioester linker, which can be hydrolyzed selectively under mildly acidic conditions (pH ∼ 5.3) at a slow rate, thus enable controlled release of guest molecules. Biological evaluation revealed that doxorubicin loaded cross-linked nanoassemblies (CNs-DOX) are nontoxic to normal cells such as HEK-293 or PBMC, but in contrast, showed a robust apoptotic effect on colon cancer cells, HCT-116, indicating excellent specificity. Thus, the fabrication reproducibility, robust stability, triggered drug release and cell selective toxicity behavior make this small molecular system very promising in the field of chemotherapeutic applications. © 2019 The Royal Society of Chemistry.