The autotoxicity of root exudates is an important factor that affects soil enzymes and microbes in rhizosphere soil. Previous studies have confirmed that 2,4-di-tert-butylphenol (2,4-DTBP) is a major autotoxin of the root exudates that severely hampers the yield and quality of Lanzhou lily. However, little is currently known regarding the mechanism of 2,4-DTBP. Here, we hypothesized that 2,4-DTBP has a direct effect on soil functionality and the microbial community structure in Lanzhou lily rhizosphere soil, thereby affecting the growth of Lanzhou lily. To test our hypothesis, various experiments were conducted in this study. We treated Lanzhou lily plants with 2,4-DTBP at different concentrations and analyzed the effects of 2,4-DTBP on rhizosphere soil enzyme activity and microbial community structure and function. The diversity of soil microbes was analyzed using high-throughput sequencing. The results showed that 2,4-DTBP altered rhizosphere soil enzyme activity and microbial community structure and function. Moreover, microbial biomass was stimulated with the addition of 0.5 mM 2,4-DTBP and inhibited with the addition of 2.0 mM 2,4-DTBP. Thus, the 2.0 mM 2,4-DTBP treatment was not suitable for the growth of soil microorganisms. We also found that the 2.0 mM 2,4-DTBP treatment resulted in an increase in the levels of fungal pathogens, such as Fusarium, and reduced the size of beneficial bacterial populations in the rhizosphere soil. Moreover, the effects of 2,4-DTBP on soil functionality and the microbial community structure differed based on the concentrations of 2,4-DTBP and the specific indexes of determination. Thus, we concluded that 2,4-DTBP could inhibit soil functionality and disturb the microbial community structure in the rhizosphere soil. This finding may be important for understanding the relationship between autotoxicity and barriers and clarifying the long-term continuous cropping problems of Lanzhou lily.