Low-molecular-weight oyster peptides (LOPs) are typical bioactive peptides with ameliorated immunomodulatory properties. However, the mechanism underlying its effect on immune functions and intestinal flora after chemotherapy has not been reported. In this study, Lewis lung cancer mice were used along with cytotoxic chemotherapy to establish model to investigate the ameliorative effects of LOPs on immunomodulatory function and intestinal flora structure. Our results showed that administration of LOPs alleviated weight loss, reduced spleen tissue damage, increased splenic T-lymphocytes, and markedly increased secretion of serum immunoglobulins and decreased inflammatory factors. Additionally, LOPs significantly increased the abundance of beneficial bacteria (Lactobacillus and Coriobacteriaceae_UCG) and decreased pathogenic bacteria (Clostridium) present in intestine. Hydrophobic amino acids and glutamate may be the underlying components to mitigate negative effects of chemotherapy. This study provides a theoretical basis for the use of LOPs as a nutritional base for the development of formula foods for cancer patients undergoing chemotherapy.