Heavy metals concentrated in waters can also accumulate in sediments and various biota. This research was conducted to examine the concentration of heavy metals in seawater, sediment, intestine and meat of golden sea cucumber Stichopus herrmanni in Kayeli bay, Buru Island, Indonesia. The concentrations of heavy metals Hg, Au, and Fe were analyzed using the AAS, and the tissue damage of S. herrmanni used the HE staining method. Correlation analysis and multiple linear regression were used to examine the correlation and the effect of the independent variables (heavy metals Hg, Au, and Fe) partially on the dependent variable (damage on intestinal villi of S. herrmanni) with a statistically significant at α= 0.05. The results showed that the highest to lowest heavy metal concentrations in water was Hg>Fe>Au, while the concentration of heavy metals in water, intestine and meat was of sea cucumber was Fe>Hg>Au. There was a correlation between heavy metals in sediments, intestines, and meat which caused damage to intestinal villi, while the multiple linear regression tests showed a probability of 0.012<0.05 for Fe, a probability of 0.000< for Hg, while probability >0.05 for Au on the damage of intestinal villi of S. herrmanni. This shows that Fe has a significant potential to cause damage to the intestinal villi of S. herrmanni. Fe is highly concentrated in sediments, intestines and meat showed a positive correlation to the damage of intestinal villi of S. herrmanni.