In order to investigate the ecological effects of enclosure culture on the lake ecosystem, the investigation was carried out three times in the enclosure culture of Lake Hongze and its inlets and outlets during 2018. The response mechanism of the lake ecosystem after enclosure culture demolition was analyzed based on the data accumulated by comparing the spatial distribution characteristics of water quality parameters, the phytoplankton, zooplankton, and benthos communities in different areas of Lake Hongze (estuary, lake center, enclosure area, peripheral area, and demolition area). The results show that there are obvious differences between water quality and aquatic organisms in different lake regions. The concentrations of total nitrogen, total phosphorus, and suspended particulate matter in the samples collected within the culture areas are slightly higher than samples collected in the estuary and lake center, but both density and biomass of the phytoplankton are lower in the culture areas than those in the estuary and lake center. The proportion of Cyanophyta and rotifers in the culture areas is higher than that in the estuary and lake center. This distribution difference is largely affected by external input and hydrodynamic conditions. On the contrary, the differences in water quality and aquatic organisms between various areas of the enclosure culture are not considerable, indicating that the water quality has not improved significantly in the short period after the enclosure culture is removed. And the water quality with high algae density and low transparency will be detrimental to submerged plant growth and community recovery. Therefore, it's necessary to take further rational and effective ecological restoration measures to promote the restoration of the enclosure culture ecosystems.