Collagen sponges are widely used for oral tissue regeneration, due to their extracellular matrix-mimetic architecture and excellent biocompatibility. However, in practical biomedical applications, collagen sponges may exhibit hydration-induced structural instability, and there can be associated inflammatory responses under physiological conditions, potentially compromising their regenerative performance. In this study, we investigated how two cross-linking strategies—transglutaminase (TG) and 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide/N-hydroxysuccinimide (EDC/NHS)—modulate the structural stability and inflammatory profiles of collagen sponges. TG-cross-linked sponges exhibited microstructural collapse, associated with macrophage activation and engagement of the Itgαvβ3/5–Src–RhoC–NF-κB signaling axis. In contrast, EDC/NHS-cross-linked sponges preserved a stable porous architecture, effectively suppressing this signaling cascade and establishing a low-inflammatory microenvironment. These findings elucidate a key mechanism by which cross-linking regulates the microstructural integrity of collagen scaffolds and provides in vitro-derived preliminary design principles for developing next-generation collagen biomaterials with low-inflammatory properties.