Notoginseng Radix et Rhizoma (Sanqi in Chinese) is a precious traditional Chinese herbal medicine. It has the effect of dispersing blood stasis and stopping bleeding, reducing swelling and fixing pain. However, it tends to contaminate with harmful fungi during storage, which may make it much less effective. In order to understand the fungal contamination of Notoginseng Radix et Rhizoma and master its composition of the exogenous fungi. The surface fungi of Notoginseng Radix et Rhizoma samples collected from six Chinese provinces and districts were investigated by using dilution plate method. Detection of aflatoxins by UPLC-MS/MS. The results showed that Penicillium citrinum was dominantly isolated from Notoginseng Radix et Rhizoma samples from No.1 to No.4. Aspergillus flavus, which produces aflatoxin, was dominantly isolated from Notoginseng Radix et Rhizoma samples from No.5 and No.6. In addition, kinds of mycotoxin were assayed which were produced by three of those identified A. flavus. All three fungi strains produced aflatoxin B1 (AFB1) and one strain HBSQ1-5 additionally produced other three kinds of mycotoxin, AFB2, AFG1 and AFG2. It is the results implied that it will be very important to take serious cautions when using Notoginseng Radix et Rhizoma. As well as, understanding the composition of the exogenous fungi of Notoginseng Radix et Rhizoma and the strains of toxin-producing fungi, which can play an important role in guiding the storage of Notoginseng Radix et Rhizoma.