Sclerotiorin is the secondary metabolite of Peniciilium sclerotiorum, which is usually produced by solid state fermentation or liquid culture without stirring (formation of mycelial mat on air-liquid surface). In the present work, it was confirmed that malic acid was produced during cell suspension culture in a liquid medium (mycelia acting as planktonic cells) using resting cells as whole cell biocatalyst. The accumulation of malic acid was caused by overflow carbon metabolism at high glucose concentration (Crabtree effect), which led to low ambient pH value. The low ambient pH repressed sclerotiorin biosynthesis. In order to overcome the low pH caused by Crabtree effect, many influenced factors, such as phosphate buffer system, initial pH, biomass loading, slowly metabolized carbon resource, and mixed sugars as carbon resource, were investigated. Finally, the low pH caused by Crabtree effect was eliminated by taking the advantage of carbon metabolite repression via utilization of mixed sugars (glucose and lactose) as carbon resource. And then, an ideal pH approximately 3.8 was maintained and corresponding high concentration of sclerotiorin (150 absorbance unit at 365 nm, corresponding to 1.9 g/l) was achieved by cell suspension culture with a relatively high biomass loading 11.7 g/l DCW (dry cell weight).