Extractive fermentation with nonionic surfactants is a potential method for producing Monascus pigments. In this study, the correlation between mycelium morphology and pigment production was investigated in extractive fermentation of Monascus anka GIM 3.592. The results demonstrated that pigment biosynthesis was associated with mycelial morphology and the accumulation of granular inclusions in cells. The physiological status in terms of hyphal and pellet diameters exhibited an excellent correlation with pigment accumulation, especially the yield of extracellular pigment in extractive fermentation (r > 0.85, p < 0.05). Nonionic surfactants could reduce pigment yield by influencing the morphology of hyphae and mycelium pellets. High yields of both intracellular and extracellular pigments could be achieved by controlling variations in hyphal diameters in two stage extractive fermentation. Moreover, continuous extractive fermentation led to stable pigment production, with a relatively high productivity of total pigments reaching 72.3 AU/day. This study proposed a simple method for monitoring pigment biosynthesis in extractive fermentation using mycelium morphology as an indicating factor.