A novel designed three-dimensional (3D) multi-microhole helium plasma jet device excited by nanosecond pulse is developed in atmospheric air. Systematical investigations about the discharge characteristics are carried out to get insights into the formation mechanisms of 3D plasma jets. Results show that the 3D plasma jets originated from the branching of a single ionization wave to present a hexagonal-like structure including bottom jet (BJ) and side jets (SJ1 and SJ2). The BJ always keeps a stable performance while the SJ displays a remarkably turbulent mode. The dynamic evolution, and the propagation velocity and distance for BJ and SJ demonstrate significant differences, with a delay effect between BJ and SJ bullets propagation being observed. The OES show that 3D jets possess a high yield of the spatial distribution of reactive species in jet plumes. The formation mechanism of 3D jets is determined by the hydrodynamic (He flow distribution) and electrical interactions (distribution of electric field force) in the discharge tube emerging from individual holes with different radial directions. The direct treatment of water using this developed underwater 3D plasma device results in the production of plasma activated water (PAW) with a lower pH value, higher conductivity, and greater concentrations of reactive oxygen and nitrogen species (RONS), compared to the indirect treatment. Especially, the concentration of H2O2 can remarkably increase 141 folds from 1.43 to 202.12 μM within 5 mins after the direct 3D plasma treatment. This novel-designed 3D jets-based technique is a promising platform for 3D application scenarios, especially in the case of underwater microbubble discharge, which is of great significance for water activation in emerging applications.