Background Trichoderma brevicompactum can control of plant diseases, but there are few studies about the control of root rot by T. brevicompactum 31636 and its biocontrol mechanism. Objective To explore the impact of T. brevicompactum 31636 on root rot and the structure of fungal communities of rhizosphere soil. Methods The effect of T. brevicompactum 31636 on controlling root rot was assessed, the growth of plants was observed by pot experiments, and the fungal structure was detected by high-throughput sequencing analysis. Results Compared with the CK (healthy plants) group, the plant height, fresh weight, and dry weight increased by 55.3%, 48.55% and 57.8%, respectively. While the concentration of atractylenolide I, II, III, and atractylone increased by 19.35%, 16.96%, 89.42% and 89.32%, respectively. The results of pot experiments indicated that T. brevicompactum 31636 could significantly improve the survival rate of Atractylodes macrocephala. The results of principal coordinates analysis (PCoA) showed that the sample of CK and Fo+Th (adding Fusdrium oxysporum before T. brevicompactum 31636) group on one side, and samples of Th and Fo group on the other. Furthermore, among the top 20 dominant fungi detected, the fungal genus with 1% increase of relative abundance included Trichoderma (1%), Sordariomycetes (1.5%), Mortierella (1.3%), Penicillium (1%), meanwhile the fungal genus with 1% decrease of relative abundance included Fusarium (30%) and Pleosporales (1%). Conclusion In summary, T. brevicompactum 31636 can control the root rot of A. macrocephala by regulating of the soil fungal community and inhibiting pathogen.