Cordyceps militaris is a type of entomogenous fungi and has been widely used as a medicinal fungus in Asia. Cordycepin produced by C. militaris has also been found to protect the liver. Moreover, deep ocean water (DOW) was proven to increase the functional compounds of functional fungi-fermented products. However, the regulation of the metals in DOW is still unclear. Therefore, this study investigated the effect of DOW and certain major ions on the production of cordycepin and adenosine of C. militaris. The results indicated that, compared with using ultra-pure water (UPW), using DOW to cultivate C. militaris in a submerged culture increases the production of biomass and adenosine (p < 0.05). In the results of solid culture, the concentration of DOW exhibits a dose effect on cordycepin production. DOW contains ions that can improve the effectiveness of cordycepin, such as Mg(2+), Na(+), Ca(2+), Fe(2+), and NO3 (-), whereas the ion Cl(-) features an inhibitory effect. Moreover, Mg(2+), Na(+), K(+), Ca(2+), Fe(2+), and SO4 (2-)can increase the production of adenosine, whereas Cl(-) cannot. However, the synthetic water made from various types of sodium salts (MgCl2, NaCl, KCl, CaCl2, FeCl2) had nearly the same effect on cordycepin production as that of DOW.