Fumigaclavine C (FC), which is produced by Aspergillus fumigatus, is a conidiation-associated ergot alkaloid with significant medical benefits. However, its application is restricted by low yields from submerged cultures. In this study, the technical feasibility of using molasses as a cost-effective ingredient for FC production in a two-stage culture of A. fumigatus was evaluated. The results indicated that molasses supplementation significantly enhanced FC accumulation by promoting conidiation and up-regulating hydroxymethylglutaryl-CoA reductase activity. Via the optimization of the two-stage process in the presence of molasses, FC production in shake flasks reached 226.9 mg/L, which was approximately three times that in the original medium (75.9 mg/L). The use of molasses as a cost-effective ingredient for FC fermentation was also successfully reproduced in a lab-scale bioreactor system in which the maximum FC production reached 215.0 mg/L. The FC production obtained in this study is the highest ever reported. This increased efficiency will enable large-scale production of FC and extend the application of molasses as a low-cost substrate for producing other conidiation-related secondary metabolites.