Red mold dioscorea (RMD) produced by Monascus sp. was proven to be a hypolipidemic functional food. Deep ocean water (DOW), that is, water obtained from over 200 m deep in the ocean, was found to promote the growth of fungus via its mineral richness. On the basis of the advantages, this study used 650 m DOW as the culture water to culture Monascus purpuresus NTU 568 and produce the DOW-RMD. The goal of this study is to compare the difference between DOW-RMD and reverse osmosis water-cultured RMD (ROW-RMD) on the hypolipidemic effect. Hyperlipidemic hamsters were fed a high-cholesterol diet and administered various doses of DOW-RMD or ROW-RMD for 8 weeks. After sacrifice, biochemical analyses in serum, liver, and feces were carried out. The results showed that DOW-RMD had a greater effect on lowering cholesterol levels and lipid peroxidation in serum and lipid plaque in heart aorta than ROW-RMD. However, DOW was likely to modulate the Monascus metabolite biosynthesis pathway toward the formation of hypolipidemic yellow pigments (such as monascin and ankaflavin) rather than red pigments and the mycotoxin citrinin. In addition, the DOW with higher Mg(2+) ion was proven to absorb into DOW-RMD; however, the accumulation of Mg(2+) ions should contribute a greater hypolipidemic effect to DOW-RMD. Comprehensively, the DOW-induced metabolism modulation and the ions of DOW were a benefit to the development of safe DOW-RMD with low citrinin levels and high hypolipidemic, antiatherosclerosis, and anti-fatty liver effects.