Abstract Sustainable biomass adhesives are considered one of the most promising alternatives to petroleum‐based adhesives. However, the poor strength and low toughness of biomass adhesives have hindered their commercial application. Herein, an ultra‐tough biomass adhesive with excellent applicability is successfully designed and constructed via the introduction of an aggregate nanostructure domain (NSD) as the molecular springs. Different from other energy dissipation unit, the NSD is self‐assembled from the protein with a higher content of α‐helical and β‐turn structures (P‐NSD), which is directionally induced by keratinase. The free sulfhydryl groups in P‐NSD can form bridge connections with the biomass‐based adhesive (BD) through dynamic disulfide bonds, thereby triggering the energy dissipation mechanism. In addition, P‐NSD demonstrates enhanced universality in protein‐based adhesives and can be conveniently fabricated via large‐scale utilization of waste keratin. Benefits from these enhancements, soybean meal‐based adhesive (BD/P‐NSD) as an example, shows a significant wet strength of 1.03 ± 0.03 MPa and dry strength 2.99 ± 0.05 MPa, which ranks above the urea‐formaldehyde resin. The toughness of the BD/P‐NSD films increases by 8.8 times to 0.44 MJ m −3 . This sustainable approach of enzyme‐induced self‐assembly of active nanostructured domains can be conveniently scaled up and has excellent economic benefits.