Abstract: To explore the distribution patterns and function of extracellular EPS and glycogen in cyanobacteria, we studied the carbon fluxes repartition throughout the EPS/glycogen metabolic biosynthesis pathways in Microcoleus vaginatus Gomont (FACHB-896) under nitrogen, phosphorus, magnesium, calcium and iron deficiency conditions. The results showed that the lack of \rmNO_3^- , \rmPO_4^3- and Mg²⁺ in the medium significantly inhibited the growth and the chlorophyll a synthesis of M. vaginatus (P<0.05), but the lack of Ca²⁺ and Fe²⁺ medium had no significant effects on these two indexes (P>0.05). The deficit of \rmNO_3^- , \rmPO_4^3-, Mg²⁺, Ca²⁺ and Fe²⁺ did not stimulate the secretion of RPS and total EPS (P>0.05), while the lack of Ca²⁺ and Fe²⁺ significantly promoted the synthesis of CPS (P<0.05). The deficit of \rmNO_3^- , \rmPO_4^3- , Mg²⁺, Ca²⁺ and Fe²⁺ all significantly promoted the synthesis of glycogen (P<0.01), and significantly reduced the EPS/glycogen ratio with a range of 1.7 and 8.0 (P<0.01). Nitrogen deficiency had the value of the lowest EPS/glycogen (P<0.01) and the highest intracellular total sugar (P<0.01), showing that the energy distribution in cells was more economical. The above results showed that M. vaginatus tend to store glycogen, but 1.7—8.0 times carbon flow of glycogen was still used to synthesize EPS. In the process of extracellular synthesis of EPS, the limited energy was preferentially synthesized to CPS which was beneficial to its own survival, and then to RPS secretion. Nutrient deficiency significantly affected the distribution pattern of EPS and glycogen of M. vaginatus, which may benefit its resistance to the barren desert environment.