The invasive Phytolacca americana L. poses a significant threat to local agroforestry ecosystems due to its allelopathic toxicity. However, the ecophysiological response mechanisms of crops to allelochemicals remain unclear. This study investigated the seedling growth, physiological, and biochemical responses of three gramineous crops to the root extracts of P. americana and identified potential allelochemicals of the invader. The germination and seedling growth of three crops were inhibited by extracts differently, with high-concentration extracts causing more severe inhibition on seedling roots in hydroponic (>57%) than soil culture experiments (>18%). This inhibition may be related to representative secondary metabolites such as fatty acyls, alkaloids, and phenols. Despite the significant inhibition of high-concentration extracts on seedling growth, the levels of soluble sugar, soluble protein, and antioxidant enzymes increased synergistically. Under allelopathic stress, three species enhanced antioxidant enzyme activities and metabolite contents at the cost of reducing their shoot, root biomass, and root/shoot ratio. This may be an ecophysiological growth-defense strategy to bolster their resistance to allelopathy. Interestingly, transgenic rice exhibited greater sensitivity to allelochemicals than wild-type rice, resulting in more pronounced growth inhibition and increased levels of most metabolites and antioxidant enzymes. This study highlights the adaptive strategies of three gramineous crops to the allelopathy of invasive P. americana.