The excessive proliferation of filamentous green algae (FGA) has been considered to be one of the important factors that result in poor growth or even a decline in submerged macrophytes. This study aims to investigate why FGA has stronger growth advantage than that of submerged macrophytes in the co-culture system. Assimilation of nitrogen and phosphorus nutrients, kinetics, and interspecific nutrient competition model were studied to determine the dynamic changes in nutrient assimilation between submerged macrophytes and FGA in a co-culture system with ion depletion technique. The results showed that differences were observed in the assimilation of nitrogen and phosphorus by Vallisneria natans, Ceratophyllum demersum, and Cladophora oligoclona. C. oligoclona was able to assimilate and accumulate much more nitrogen than V. natans and C. demersum, with the content of nitrogen of 5.75% (dry mass). The lower value of Michaelis-Menten constant K_m (0.34 mg/L) of C. demersum indicated that C. demersum had a greater affinity for phosphate. The interspecific competition results confirmed that the coexistence of V. natans and C. oligoclona, and C. demersum and C. oligoclona were unstable. Moreover, C. demersum had a stronger competitive ability than V. natans, and it can be used as a pioneer species for the recovery of submerged vegetation in eutrophic lakes.