Abstract: This study investigated the morphological changes of internal organs in the black sea cucumber Holothuria atra during fission and regeneration, as well as its absorption and utilization of exogenous dissolved nutrients. Fission was artificially induced by rubber band ligation, and the internal organ changes in the anterior and posterior segments were observed through dissection at 0, 10, 30, 50, and 60 days (d) post-fission. Based on stable isotope tracing, labeled dissolved amino acids (δ¹³C, δ¹⁵N) and glucose (δ¹⁸O) were added to the water at 10, 30, and 60 d of regeneration, respectively. Intact H. atra without the addition of exogenous nutrients served as the control group. The changes in isotope ratios in the body wall tissues of the intact group, anterior parts, and posterior parts were compared. Morphological observations showed that at 60 days post-fission, the anterior parts completely regenerated the intestine, respiratory trees, and cloaca, while the posterior parts reconstructed the intestine, pharyngeal complex, and tentacles. Both parts successfully restored a complete digestive system. Isotope tracing results indicated that the addition of exogenous dissolved nutrients significantly altered the isotopic composition of the regenerating body wall tissues. Compared with the control group, the δ¹⁵N values of both anterior and posterior individuals in the experimental group increased significantly at all regeneration stages, indicating effective absorption of amino acids during regeneration. The δ¹³C values in the posterior parts were significantly higher than those in the control group at 30d. Regarding glucose absorption, the δ¹⁸O values of the anterior tissues were significantly higher than those of the posterior tissues after adding exogenous nutrients, suggesting potential differences in absorption efficiency or metabolic pathways between the different body sections. The study demonstrates that H. atra requires 60 days to complete the full remodeling of the digestive system and respiratory trees following fission. Both dissolved amino acids and glucose can be absorbed during regeneration, with the anterior segments exhibiting a higher glucose uptake than the posterior segments. This study confirms that dissolved organic matter (DOM) is a crucial exogenous nutritional supplement during the regeneration of H. atra, revealing the differential utilization of exogenous nutrients across various regeneration stages and body parts. These findings provide a theoretical basis for elucidating the energy allocation strategies and nutritional compensation mechanisms in echinoderm regeneration.