Codonopsis pilosula, an important genuine herb in Shanxi Province, is generally named Lu Dangshen, and is well-known for its high medicinal value. In 2023, Fusarium wilt, a newly observed severe disease on C. pilosula, is responsible for approximately 40% incidence in the field. It was noticed that the diseased C. pilosula roots were usually asymptomatic on the surface. The typical symptoms were vascular discoloration, wilt, and leaves chlorosis. A total of 87 Fusarium isolates were isolated from diseased samples, and identified as Fusarium oxysporum based on morphological features and partial sequences analyses of internal transcribed spacer region of ribosomal DNA (ITS-rDNA), translation elongation factor 1 alpha (TEF-1α) and endopolygalacturonase 1 (pg1). Of the 87 Fusarium oxysporum isolates, the causal agents were separated into three distinct groups (Groups I, II and III). The virulence of each F. oxysporum isolate to C. pilosula was determined by measuring the disease incidence and Fusarium wilt severity. All the 87 Fusarium oxysporum isolates could cause typical symptoms similar to that originally appeared on diseased plants, and present significantly different pathogenic to C. pilosula. All tested isolates were highly sensitive to jinggangmycin, azoxystrobin, fludioxonil and epoxiconazole (EC50 < 10 μg/mL), and insensitive to iprodione and hymexazol. Additionally, F. oxysporum isolates have a low risk for fungicide resistance to jinggangmycin, iprodione and epoxiconazole. Thus, jinggangmycin and epoxiconazole should be recommended for the control of this disease. Our finding in this study should be useful for the understanding of Fusarium wilt of C. pilosula caused by F. oxysporum.