Changes of the collagen in sea cucumber (Stichopus japonicas) during cooking were investigated. Crude collagen fibers (CCF) is more sensitive to heat than pepsin-solubilized collagen (PSC), absorbance at 226-232 nm increased from 60 to $100^{circ}C$. PSC nearly completely degraded after cooking for 8-10 h, 4-6 h, 1-1.5 h, 40-50 min, and 10-20 min at 60, 70, 80, 90, and $100^{circ}C$, respectively. Collagen fiber shrinkage, disappearance of periodic cross striation, complete denaturation, and dispersion of denatured fibers at 40, 60, 80 and $100^{circ}C$, respectively, were demonstrated by transmission electron microscope (TEM). Above results might be instructional for sea cucumber processing and collagen usage.