Natural polymer-based hydrogels attract great attention because of their inherent biocompatibility and controllable biodegradability. However, the broad applications of these hydrogels require a combination of high mechanical strength, high toughness, fatigue resistance, as well as self-healing. The integration of this combination into one natural polymer-based hydrogel remains challenging. Here, a molecular design strategy was proposed to fabricate mechanically robust silk fibroin-based hydrogels using host−guest interactions. Silk fibroin molecules was chemically modified with cholesterol (Chol, guest) or β-cyclodextrin (β-CD, host), and host−guest interaction between Chol and β-CD moieties drove the supramolecular assemblies of hydrogels. The dissociation/ reassociation behavior of host−guest complexation, serving as sacrificial bonds, endowed hydrogels with effective energy dissipation and rapid self-healing ability. The prepared silk fibroin-based hydrogels exhibited high mechanical strength, high toughness, and remarkable fatigue resistance, superior to conventional silk fibroin hydrogels. Moreover, due to reversible host−guest interactions, hydrogels achieved facile functional recovery after damage without any external stimuli. This design strategy provides an avenue to develop natural polymer-based materials with robust mechanical properties, thus broadening current hydrogel applications.