Selenium (Se) is a trace element that plays a crucial role in metabolism; a lack of selenium reduces the body’s resistance and immunity, as well as causes other physiological problems. In this study, we aim to identify favorable conditions for improving organic selenium production. The functional microbe Monascus purpureus, which is widely used in food production, was employed to optimize selenium-enriched culture conditions, and its growth mode and selenium-enriched features were investigated. Spectrophotometry, inductively coupled plasma optical emission spectrometry (ICP-OES), and HPLC (High-Performance Liquid Chromatography) were used to determine the effects of various doses of sodium selenite on the selenium content, growth, and metabolism of M. purpureus, as well as the conversion rate of organic selenium. The best culture parameters for selenium-rich M. purpureus included 7.5 mg/100 mL of selenium content in the culture medium, a pH value of 6.8, a culture temperature of 30 °C, and a rotation speed of 180 rpm. Under ideal circumstances, the mycelia had a maximum selenium concentration of approximately 239.17 mg/kg, with organic selenium accounting for 93.45%, monacoline K production reaching 70.264 mg/L, and a secondary utilization rate of external selenium of 22.99%. This study revealed a novel biological route—selenium-rich M. purpureus fermentation—for converting inorganic selenium into organic selenium.