Pen culture has been widely developed in most frestwater lakes in China and a higher fish yield of 7500 kg/hm² was achieved in some grass-type lakes during the implementation of the 8th Five-year Plan. In East Taihu Lake, the fish yield has now kept increasing with the increase of stocking fingerlings, feeding rate and collecting aquatic weeds, but such practice leads to the unbalance of nitrogen and phosphorous budget and causes a negative impact on the aquatic environment. However, it is somewhat difficult for the government to conduct an effective measurement to control the practice for the time being because of its benefits for the fish farmers. Hence, it is necessarily important to study the ecological practice of pen culture in the grass-type lakes for the proper maintenance of natural resources and protection of the benefits of fish farmers. The study was conducted in Miaoguan, East Taihu Lake with a total pen area of 10 hectare (hm²), where crab and fish were polycultured. In this study, both nitrogen and phosphorous elements were negatively increased through the proper control of feed loading during the culture period . This practice was considered as an ecological cultural model for the sustainable aquaculture development in lakes. The experiment was conducted to study the effects of polyculturing fish with crab in pens on the level of nitrogen and phosphorous in the lake water. With the calculation of input and output of nitrogen and phosphorous during the culture, the experimental results show that the model of polyculture of with crab in pens did not increase the level of nitrogen and phosphorous in the lake water, but it partially reduced their levels instead. During the whole production season, the input of nitrogen and phosphorous by both stocking of fish and crab seeds and loading of feed was 27. 889kg·hm^-2 and 4.381 kg·hm^-2, respectively; while the output of nitrogen and phosphorous by harvesting of fish and crab was 41.177 kg·hm^-2 and 5.801 kg·hm^-2, respectively. As a result, the level of nitrogen and phosphorous could be reduced at a rate of 13.288 kg·hm^-2 and 1.420 kg·hm^-2, respectively from pen culture in the lake. In conclusion, such culture model may result in ideal economic efficiency, low impact on the community of aquatic organisms, thus favoring the sustainable development of pen culture in lakes.