Our previous work indicated that secalonic acid F (SAF) was the major allelochemical produced by Aspergillus japonicus. Studies showed that SAF markedly inhibited the seedling growth of sorghum (Sorghum vulgare Pers.), hairy beggarticks (Bidens pilosa L.), and barnyardgrass (Echinochloa crus-galli (L.) Beauv.). It significantly reduced the activities of superoxide dismutase (SOD) and peroxidase (POD) at a concentration of 0.3 mM. Secalonic acid F enhanced malondialdehyde (MDA) contents, but it lowered the content of chlo-rophyll (CHL) a and b as well as the photosynthetic rates of tested plants. Respiration, membrane permeability, and abscisic acid (ABA) content increased after treatment with SAF, but the reduction activity of the root system was lowered. There is no remarkable change in the soluble proteins of plants that are treated with SAF. Transmission electron microscope (TEM) observations showed that treated plants exhibited amorphous mitochondria without integral membranes and swelling chloroplasts without membranes in a disorderly arrangement. The SAF treatment also damaged the stratiform structure of the chloroplasts and the membranes and structure of the nuclei. These tissues against membrane lipid peroxidation and damage the whole membrane system of plants, resulting in the ultrastructure destruction of chloroplasts, mitochondria, and nuclei. Cell ultrastructure destruction causes a reduction of photosynthesis and root activities and an increase in respiration. These abnormal physiological processes contribute to the inhibition of plant growth.