Abstract: The aim of these experiments was to determine the effects of cotyledon damage on the growth of Sophora alopecuroides, a native invasive species in the Ili River Valley of Xinjiang. To simulate cotyledon predation, cotyledons were cut with different degrees of severity (excision of half a cotyledon, half of two cotyledons, one cotyledon, 1.5 cotyledons, and two cotyledons) or left uncut (control), and the growth of the seedlings was evaluated. The mortality rate, plant height, and leaf area strongly depended on the degree of cotyledon damage. There were no significant differences in seedlings’ taproot length among the damaged and non-damaged treatments. Compared with the control, the seedlings with 1.5 and two damaged cotyledons formed significantly fewer and shorter lateral roots, while those with half or one damaged cotyledon showed no significant difference in lateral root formation. Cotyledon damage significantly decreased the stem biomass, leaf biomass, and total biomass of seedlings, but had only small effects on the root biomass and root∶shoot ratio. As the severity of cotyledon damage increased, biomass allocation to the stem was unaffected, biomass allocation to the root significantly increased, and biomass allocation to the leaf significantly decreased. These results indicate that cotyledon damage is a bottleneck in seedling establishment and population regeneration.