The growth of filamentous microorganism is contributed by tip extension and branching. The microscopic growth of filamentous microorganism means the growth process from one or a few spores. In order to describe the microscopic process, a population morphologically structured model is proposed, in which three morphological compartment and their interactions were considered, and the heterogeneity of hyphal growth was included. The model was applied to describe the microscopic growth of Streptomyces tendae and Geotrichum candidum with good agreement. From model prediction, it is concluded that if the number of hyphae is large enough (macroscopic growth), the specific growth rate of filamentous microorganism and the ratio of morphological forms in hyphae will become constant.