Phosphorylation and calcium cross-linking are important factors affecting the gel properties of sea cucumber collagen aggregates. A texture profile analysis (TPA), a stress relaxation experiment, low field nuclear magnetic resonance (LF-NMR), and Van Gieson staining were performed to investigate the textural characteristics, moisture migration, and changes in chemical bonds as well as in the characteristics of collagen fibers of phosphorylated and calcium cross-linked collagen gels. The results showed that phosphorylation with 2% sodium tripolyphosphate adversely affected the gelling properties of sea cucumber collagen aggregates. Compared with the control group, the phosphorylated collagen aggregates had lower viscosity, chewiness, η1, E1, and bound water content, and higher free water content and water activity (Aw). Calcium crosslinking (with 1% calcium chloride) after phosphorylation had a significant impact on the gelling properties of sea cucumber collagen aggregates, resulting in greater hardness, higher viscosity, and lower Aw. The degree of binding between collagen aggregates and water increased and the gelling properties were enhanced, thus leading to a more stable structure of collagen fibers. Compared with the high pressure and high temperature treatment, the combination of calcium crosslinking and phosphorylation can improve the gelling properties of sea cucumber collagen fibers, and provide a new route for the processing and performances of sea cucumbers.