Engulfment and cell motility protein (ELMO) was identified as a novel, evolutionarily conserved upstream regulator of the RAC signaling pathway in mammals, which was essential for diverse physiological and pathological processes of cells, such as phagocytosis and cell migration. However, the functions and the underlying mechanisms of ELMO1 are generally poorly understood in invertebrates. In this study, we found that the endocytosis and GTP activity were significantly enriched in AjELMO1-interfered coelomocytes of Apostichopus japonicus by RNA-seq. Moreover, overexpression or interference of AjELMO1 significantly altered the coelomocyte phagocytosis levels induced by Vibrio splendidus AJ01, leading to an increase and decrease in the intracellular AJ01 burden by flow cytometry and bacteriophage plate counting in vivo and in vitro. Further functional analysis with different endocytosis inhibitors treatment revealed that AjELMO1 mediated AJ01 internalization via the actin-dependent endocytic pathways through the changes of F-actin/G-actin, but not the clathrin-, macropinocytosisi-, and dynamin-dependent endocytic pathways. The dedicator of cytokinesis protein 1 (AjDOCK180) was identified as an interacting protein of AjELMO1 using co-IP and GST-Pull down followed by mass spectrometry identification. Further function analysis also revealed that AjDOCK180 promotes coelomocyte phagocytosis through the actin endocytosis pathway via the changes in the phagocytosis levels, the intracellular AJ01 burden, and the ratio of F-actin/G-actin in coelomocytes. Additionally, we found that the phagocytic activity in sea cucumber coelomocytes promoted by AjELMO1 can be blocked by interference with AjDOCK180. Altogether, our data demonstrate that AjELMO1-AjDOCK180 is involved in resisting AJ01 infection via medicating coelomocyte phagocytosis through the actin-dependent pathway.