Abstract: It is of great significance to grow the strain into the appropriate pellet form for the industrial fermentation of filamentous fungi. The morphology control in the seed culture process of Rhizopus oryzae in the 5L stirring bioreactor was investigated. The optimal conditions for the pellet formation were as follows：the spore concentration in the fermentor should be controlled in the range of （5×104）～（8.3×104）/mL, the best agitation speed was 350r/min, the best pH in the medium was maintained at 2.80, and by using residual glucose concentration of 20g/L as an empirical value the best seed age was determined at 52h. In this way, the smooth compact pellets with the diameter around 1mm were obtained. Fermentation results showed that the pellet morphology was more beneficial to the fumaric acid production than the filamentous morphology.