The mycelial morphology and the production of mycelia and exo-biopolymer by Cordyceps sinensis 16 were investigated under different culture conditions. The mycelial morphology of C. sinensis 16 was characterized by image analysis. Some variations in morphological factors and exo-biopolymer production were observed under the different culture conditions, e.g., the initial pH and agitation speed. The initial pH had a significant effect on the morphology and on the production of mycelia and exo-biopolymer by C. sinensis 16 in submerged culture. At an initial pH of 5.0, the maximal hyphal length, the number of tips, and the mycelia concentration were determined. The agitation speed was an important factor for exo-biopolymer production in terms of controlling the growth and morphology of C. sinensis 16 in the bioreactor culture. In bioreactor cultures, as the agitation speed was increased, rapid differentiation and cell lysis occurred; at 350 rpm, a mycelial concentration of 62.3 g/L and an exo-biopolymer concentration of 22.0 g/L were obtained. This study demonstrates that, in submerged C. sinensis 16 cultures, morphological factors can be applied to efficiently produce mycelia and exo-biopolymer