Edible and medicinal plants (EMPs) are widely used but are easily infected by harmful fungi which produce mycotoxins. Herein, 127 samples from 11 provinces were collected to investigate 15 mycotoxins based on geographic, demographic, processing, and risk characteristics. A total of 13 mycotoxins were detected, and aflatoxin B1 (0.56~97.00 μg/kg), deoxynivalenol (9.41~1570.35 μg/kg), fumonisin B1 (8.25~1875.77 μg/kg), fumonisin B2 (2.74~543.01 μg/kg), ochratoxin A (0.62~19.30 μg/kg), and zearalenone (1.64~2376.58 μg/kg) occurred more frequently. Mycotoxin levels and species were significantly different by region, types of EMPs, and method of processing. The margin of exposure (MOE) values was well below the safe MOE (10,000). AFB1 exposure from Coix seed and malt consumption in China was of high health concern. The hazard Index (HI) method showed the range of 113.15~130.73% for malt, indicating a public health concern. In conclusion, EMPs should be concerned because of the cumulative effects of co-occurred mycotoxins, and safety management strategies should be developed in follow-up studies.