In this study, we investigated the relationship between the morphology and the rheological properties of Penicillium citrinum to improve the production of neo-fructosyltransferase (neo-FTase). In a 2.5 L bioreactor culture of P. citrinum, it was observed that agitation speed and aeration rate had significant effects on the production of neo-FTase and that maximum cell mass and neo-FTase production obtained at 500 rpm and 1.5vvm were 8.14 g/L and $53.2{ imes}10^{-3} U/mL$, respectively. Cell mass and neo-FTase production increased to 91.53 and 25.17%, respectively. In the morphology and rheology studies, P. citrinum showed a typical pellet morphology that was explained by a shaving mechanism; this phenomenon was significantly affected by carbon sources. The rheology of neo-FTase fermentation by P. citrinum was dependent on cell growth and fungal morphology.