Continuous cropping obstacle is the bottleneck of medicinal plant cultivation, which seriously affects the quality and yield of medicinal materials. The research on the mechanism of continuous cropping obstacle has evolved from soil physical and chemical properties and allelopathy in the 1970s to the changes of rhizosphere microenvironment and plant response mechanism at present. According to the available studies in this field and our previous research work, we systematically analyzed the mechanism of rhizosphere exudate-mediated microbial community reconstruction in the soil of the medicinal plants in continuous cropping. Specifically, rhizosphere exudates, providing the carbon source and energy for microbial growth, act as inducers or repellents to induce microbial growth or transfer, thereby changing the physicochemical properties (such as acidity) of rhizosphere soil and further altering the structure of rhizosphere microbial community. Further, we comprehensively discussed the ways of synergism between rhizosphere exudates and soil microorganisms in causing harm to the medicinal plants in continuous cropping. That is, rhizosphere exudates mediate the infection of the rhizosphere by pathogenic microorganisms, increase the susceptibility of the nearby plants, inhibit the defense of the host plants, and protect the pathogens to occupy the dominant niche. The synergistic interaction results in the release of more pathogenic factors such as mycotoxins by rhizosphere pathogens, enhanced toxicity of rhizosphere allelochemicals, and deterioration of soil physical and chemical properties. This paper summarizes the role of interaction between rhizosphere exudates and soil microorganisms in the formation of continuous cropping obstacles, aiming to provide a new research idea for revealing the formation mechanism as well as the theoretical support for overcoming continuous cropping obstacles of medicinal plants.