<p>Allelopathy is one of the important mechanisms for the spread and expansion of invasive alien plants. The current research mainly focuses on interspecific allelopathy, while there are relatively few studies on intraspecific allelopathy. <i>Solanum rostratum</i> Dunal is an annual invasive plant with strong invasiveness, the secondary metabolites produced by the litter of <i>S. rostratum</i> can accumulate in the soil, and may affect the growth of its own seedlings. Therefore, it is of great significance to clarify the intraspecific allelopathy of <i>S. rostratum</i> for understanding the invasion mechanism or proposing new prevention and control strategies. In this study, the extract of <i>S. rostratum</i> litter was used to treat its seedlings, and the soil physical and chemical properties, soil metabolites, and soil microorganisms were measured to analyze their correlation with the growth of seedlings. The results showed that 0.1 and 1&#xa0;g L^− 1 treatment significantly promoted the leaf area and biomass of seedlings, while 10&#xa0;g L^− 1 treatment significantly inhibited plant height, leaf area index, biomass, net photosynthetic rate, transpiration rate, and stomatal conductance. Some bacteria, such as <i>Brevundimonas alba</i>, <i>Brevundimonas</i>, <i>Altererythribacter</i>, <i>Novosphingobium resinovorum</i>, and <i>Novosphingobium</i> exhibited a higher abundance under 10&#xa0;g L^− 1 treatment, showed a negative correlation with seedling growth. And 25 metabolites detected in the soil, such as 2-Aminobenzoic acid, 2, 6-dibromophenol and palmitaldehyde, could as autotoxins for subsequent functional validation. The results can not only supplement the invasion mechanism of invasive plants from the perspective of intraspecific allelopathy, but also provide theoretical support for formulating control strategies for the <i>S. rostratum</i>.</p>