Previous work has shown that in many filamentous fungi fermentations the morphology of the fungi influence both biomass and metabolites. The formation of large pellet is the main characteristic of the mushroom mycelium submerged culture. In this paper the dynamic change of mycelium aggregation process was investigated in 5L fermentor. Low agitation intensity resulted in large loose mycelium aggregates rapidly and the mycelium fragment concentration (mfc) dropped to 20% of the initial value at 100 rpm at 4th h. In contrast, high agitation intensity led to small compact mycelium aggregates. A novel scheme using intermittent agitation could maintain a higher level of mfc for more than 24 h and also enhanced the production of mycelium biomass.