Mucositis is a common problem that results from cancer chemotherapy and is a cause of significant morbidity and occasional mortality. Its prevention and successful treatment can significantly enhance the quality of life of patients and improve their survival. Sea cucumber is a traditional aquatic food that has both nutritional and medicinal value. The polysaccharide fucoidan from the sea cucumber (SC-FUC) has various bioactivities. We examined the protective effect of different molecular weights (MWs 50 kDa-500 kDa) of fucoidan from the sea cucumber, Acaudina molpadioides, in a mouse model of cyclophosphamide (Cy)-induced intestinal mucositis. Results showed that the oral administration of SC-FUC markedly reversed Cy-induced damage in the mice. The sea cucumber fucoidan notably increased the ratio of the length of the intestinal villus to the crypt depth and ameliorated the IFN-γ/IL-4 ratio that signifies Th1/Th2 immune balance. Moreover, all the fucoidans in this study enhanced the expression of IgA by accelerating the expression of IL-6 that is probably combined with IL-10. The differing effects of the varied molecular weights of fucoidan may be due to the difference in the efficiency of absorption. This is a novel study on the potential preventive effects of SC-FUC on intestinal mucositis that may be related to the efficiency of its absorption during digestion. Sea cucumber fucoidan (SC-FUC) may be used as a potential food supplement to prevent chemotherapeutic mucositis.