Apostichopus japonicus is a highly significant marine aquaculture species. Research findings have indicated that male sea cucumbers demonstrate a more rapid growth rate compared to females, underscoring the potential advantages of establishing an all-male population. In this study, we identified a specific protein-coding gene (ORFan) within a 4565 bp male fragment and named it sex determination factor (sdf). The sdf transcript exhibited ubiquitous expression in various adult male tissues, along with dynamic expression patterns in the testis across different developmental stages. Notably, knockdown of the sdf gene through immersion of embryos in its specific vivo-morpholino oligomers (vivo-MO) resulted in significant changes in the expression levels of several sex-related genes including piwi1, vasa, foxl2, and DNMT3. Additionally, a transcriptomic analysis showed that sdf knockdown resulted in significant alterations in multiple biological processes encompassing various sex-related gene ontology terms such as male gonad development, ovarian follicle development, and steroidogenesis. These results provide a molecular foundation for comprehending ORFans in sea cucumbers while offering a valuable method for gene knockdown studies in echinoderms.