Natural materials instruct that mechanical consumption interactions can address the conflict between strength and toughness and enable the preparation of high-performance artificial nanocomposites. Imitating the natural spider silk structure has led to numerous strong and tough biomimetic materials through hydrogen-bond (H-bond) cross-linking; however, the relevance of H-bond cross-linking to the microstructure and mechanical performances of the nanocomposites still remains unclear. Inspired by spider silk, here we fabricate strong and tough poly(ε-caprolactone) (PCL) nanocomposites with graphene nanodots (GNDs) as reinforcements. Under the weak H-bond crosslinking, the resultant GNDs/PCL nanocomposite films with 2.0 wt % fillers show a high strength of 33.9 MPa (by ca. 82%), in combination with a significant enhancement in the modulus (by ca. 46%), toughness (by 2.2-fold), and thermal stability. Our work reveals the controlling effect of weak H-bond cross-linking on the microstructure and macroscopic performances of GNDs/PCL nanocomposites and the relationship to mechanical properties and thermal stability for the first time. This concept provides many opportunities to construct superior polymer nanocomposites for applications in the tissue engineering fields.