Roridin E, produced by Podostroma cornu-damae, is a mycotoxin with anticancer activity. To increase the content of roridin E, submerged culture conditions were optimized using response surface methodology. Three factors, namely, medium initial pH, incubation time and agitation speed were optimized using a Box–Behnken design. The optimum submerged culture conditions to increase the content of roridin E included a medium with an initial pH of 4.0, an incubation time of 12.90 days, and an agitation speed of 63.03 rpm. The roridin E content in the submerged culture, under the aforementioned conditions, was 40.26 mg/L. The findings of this study can help lower the current price of roridin E and promote its related research.