During the restoration of eutrophic shallow lakes, submerged macrophyte recovery is often accompanied by an excessive proliferation of filamentous green algae (FGA). This can lead to the recession or even disappearance of the submerged macrophytes in these lakes. However, the use of plant fragments in reproduction and dispersion is an important life history strategy for submerged macrophytes. In this work, it studied apical fragment propagation in Myriophyllum spicatum and its physiological and biochemical responses to the decomposing liquid of Cladophora oligoclona. Myriophyllum spicatum apical fragments showed no new roots or buds when treated with 0.4 times the original decomposing liquid, and their PSII functional parameters were lower than those of the control. In contrast, the relevant sugar content accumulated to 115.26%, and the activities of an energy enzyme (Ca2+/Mg2+-ATPase) and a secondary metabolic-related enzyme (PAL) increased by 490.63% and 28.13%, showing an elevated defense response. These results indicated that the early regeneration of M. spicatum could be hindered by environmental stress, and that this may further affect the reproduction and colonization of these submerged macrophytes.