The invention provides a method for evaluating the safety of aquatic environment for genetically modified insect resistant rice. The method comprises the following steps of: arranging and managing genetically modified paddies and non-genetically modified paddies; determining foreign protein in water layers and silt of the paddies, which comprises pretreating samples and extracting and determining the foreign protein; separating plankton in the water layers of the paddies, which comprises collecting water samples and precipitating and separating the plankton; determining the kind and the abundance of the plankton in the water layers of the paddies, which comprises identifying living bodies and counting the number; and planting the genetically modified insect resistant rice and evaluating the safety of the plankton, performing statistical analysis on the kind, the number and the occurrence period of the plankton by using analysis software so as to obtain parameters of a diversity index, a uniformity index and the like, and comparing the parameters with those of conventional paddies so as to evaluate the safety of the aquatic environment for the genetically modified 53 insect resistant rice. The method disclosed by the invention has practical application value for systematically assessing the safety of the aquatic environment for the genetically modified insect resistant rice.