Filamentous fungi have been extensively used in industrial fermentation processes. One of the most interesting topics of filamentous fungi is their bothersome morphology, which closely correlates with the productivity and broth rheology. Aiming at the optimization of the microbial process, works mainly focused on the relationships between morphology, productivity and environment in the last decades. Based on those works, we tried to interpret the mechanism of filamentous fungi growth from physiological aspects, and reviewed the mathematical models describing the hyphal growth, differentiation during the formation of target products. Above all, efficient and effective morphology controlling strategies were addressed from the engineering view.