Sea cucumbers suffer from non-enzymatic deterioration during heat processing and storage, which significantly devaluates the product. In the present investigation, it was found that ι-carrageenan oligosaccharide (ι-CO) synergized with Ca2+ is able to protect sea cucumbers from deterioration. The textural strength and water-holding capacity of the sea cucumber body wall were improved after treatment with ι-CO and Ca2+, and the collagen structure was more resistant to destructive experiments. In addition, pepsin-solubilized sea cucumber collagen (SCC) was extracted and demonstrated that the positive effect was due to co-gelation between ι-CO and collagen supported by rheological and thermal property studies. Furthermore, molecular dynamics simulations confirmed that ι-CO spontaneously binds to SCC, while Ca2+ promotes the crosslinking strength of the ι-CO-SCC mixed gel and enhances its water-holding capacity and mechanical strength. Therefore, the ι-CO/Ca2+ can permeate and stabilize collagen hydrogel, which provides valuable information for the development of new food additives to improve the texture of collagen-based foods.