| Algae blooms are one of the key issues inhibiting development of Eriocheir sinensis aquaculture. Cultivation of submerged plants, especially Elodea nuttallii, in E. sinensis culture ponds provides a new approach for controlling algal blooms in crab ponds. However, traditional planting of E. nuttallii limits inhibition of algae blooms. To better prevent and control algae blooms in crab culture ponds, we explored a new management approach and provide data and new ideas for improving cultivation of E. nuttallii. The experiment was carried out in crab breeding ponds from June 10 to October 25, 2017 in the Shanghai Songjiang district. Two E. nuttallii planting trials were set in triplicate. In the treatment group, plant height was limited to 30 cm and in the control group, plants were 20 cm below the water surface. The six experimental ponds were semi-closed with an area of 0.5 hm2. In February, E. nuttallii was planted to cover of 60% of the pond surface and reached 95% before the trial began. E. sinensis were released into the pond in March at a density of 9000 ind/hm2. During the experiment, E. sinensis were fed once a day, as usual, and harvesting of E. nuttallii was based on plant growth. Water quality in each pond was monitored twice in June and October, and at irregular intervals in July, August and September, according to phytoplankton level and water color. After the trials were completed, the relationship between Chl-a concentration and the physicochemical water quality parameters was analyzed by regression analysis. The average concentration of Chl-a in the control group was 4.66 times higher (P<0.01) than that of the treatment group. TP, PO4-P, T, pH, DO, and SD in the control group were significantly higher than those in the treatment group (P<0.05). The concentration of Chl-a in the control and treatment groups both presented a significantly positive correlation with TP, PO4-P, T, pH, DO, and a significantly negative correlation with SD (P<0.01). There was also a significant positive correlation of Chl-a with NO3-N in the treatment group (P<0.05). Chl-a was not correlated with CODMn, NH4-N, NO2-N, TN, TN/TP in either group (P>0.05). These findings indicate that increased nutrient concentrations, especially TP and PO4-P, will promote algal growth. The management of E. nuttallii planting in the treatment group demonstrated more effective prevention and control of phytoplankton growth in intensive culture ponds of E. sinensis and ecological cultivation was achieved.