Phthalate acid esters (PAEs) are the most frequently utilized synthetic chemical compounds worldwide. They are typical emergent contaminants and are currently attracting considerable concern due to their risks to plants, animals, and public health. Determining the vital environmental factors that affect the toxicity of target pollutants in soil is important for vegetable production and the maintenance and control of soil productivity. We investigated the influence of di-n-butyl phthalate (DBP) and bis(2-ethylhexyl) phthalate (DEHP) under different soil conditions on physiological changes in water spinach (Ipomoea aquatic Forsk.) seedlings and the rhizosphere soil microbial community. Supported by our former experiments in which we determined the representative concentrations that caused the most pronounced toxic effects, three experimental concentrations were studied including control soils without PAEs and spiked soils with either 20 mg DBP or DEHP kg⁻¹ soil. The soil at all the three PAE concentrations was then adjusted to test two soil pH values, three levels of soil organic matter (SOM) content, and three levels of soil moisture content; thus, we completed 12 treatments or conditions simulating different soil environment conditions in greenhouses. After 30 days of cultivation, we analyzed the toxicity effects of two target PAEs on plant growth and physiological factors, and on soil microbial community characteristics. The toxicity of soil DBP and DEHP to the physiology of water spinach was found to be most affected by the soil pH value, then by SOM content, and least of all by soil moisture. The results of the 454 high-throughput sequencing analysis of the soil microbial community indicated that the toxicity of target PAEs to soil microorganisms was most affected by SOM content and then by soil moisture, and no clear relationship was found with soil pH. Under different soil conditions, declines in leaf biomass, chlorophyll a content, and carotenoid content—as well as increases in free amino acid (FAA) content, superoxide anion free radical activity, and hydroxyl radical activity—occurred in response to DBP or DEHP. Heavy use of chemical fertilizer, organic fertilizer, and high humidity led to the special environmental conditions of greenhouse soil, constituting the main conditions considered in this study. The results indicate that under the special highly intensive production systems of greenhouses, soil conditions may directly influence the effects of pollutant phytotoxicity and may thus endanger the yield, nutrient content, and food safety of vegetables. The combined studies of the impacts on plants and rhizosphere microorganisms give a more detailed picture of the toxic effects of the pollutants under different soil conditions.