The responses of sea cucumbers to salinity changes are reflected in the expression profiles of multiple genes and microRNAs. The miR‐2008 and Pleckstrin Homology Domain Containing A3 (PLEKHA3) were previously shown to be involved in responses to salinity changes in sea cucumbers. To better understand the relationship between miR‐2008 and PLEKHA3, the miR‐2008 and PLEKHA3 predicted interaction was investigated using luciferase reporter assays and gene knockdowns. Dual‐luciferase reporter gene analysis indicated that miR‐2008 overexpression decreased luciferase activity in the PLEKHA3‐WT group. The miR‐2008 expression in coelomocytes was increasingly downregulated in the agomir group with salinity acclimation. PLEKHA3 expression patterns in the miR‐2008 agomir group were upregulated after 6 and 48 h and downregulated after 24 h of low‐salinity stress. The miR‐2008 expression in the miR‐2008 agomir group peaked after 24 h of low‐salinity exposure in sea cucumbers. miR‐2008 overexpression and PLEKHA3 inhibition affected ion concentrations, osmotic pressure, Na+/K+‐ATPase (NKA) activity, and ROS levels. The changes in ion concentrations, osmotic pressure, and NKA activity after 6–24 h of salinity stress were observed. The results indicated that 6–24 h after the initiation of salinity stress may be critical to the salinity‐acclimation process in sea cucumbers.