Abstract: In this paper, the concept, mechanism and action mode of allelopathic autotoxicity of medicinal plants were discussed. The study identifies that the basic reason for the continuous cropping obstacles and allelopathic autotoxicity of medicinal plant is the homology of autotoxic-allelochemicals and pharmaceutical active substances.Accordingly, the relationship between the causes of the obstacles and the autotoxicity of allelochemicals in medicinal plants are also analyzed. Comprehensive agronomic methods based on rhizospheric soil microflora systems research using DGGE, T-RFLP and other related techniques are proposed. This reduces the inhibiting effect of continuous cropping obstacles and allelopathic autotoxicity