The invention relates to a complex enzyme preparation for sludge removal and in-situ ecological remediation of organisms in eutrophic water areas, which is prepared by mixing complex enzyme and mineral water, wherein the weight ratio of the complex enzyme to the mineral water is 1:9-50. The complex enzyme comprises the following components in volume content: 50-80mg/L of bromelain, 50-80mg/L of papain, 15-30mg/L of L-aspartase and 15-30mg/L of glutathione. The invention improves the water quality of water bodies, decomposes the organic sludge deposited at the water bottom, forms dynamic balance with the continuously input pollution sources, basically solves the problem of eutrophication of water bodies, and simultaneously solves the problem of secondary pollution of sludge removal of river channels and lakes.