In order to clarify the alleviating effect of heterologous double-root on coffee continuous cropping obstacle, the soil of the continuous cropping obstacle garden of coffee was used to cultivate Caffea liberica, No. 1 and C. canephora, Reyan No. 1 heterologous double-root grafting coffee seedling. The mechanism of heterologous double-root alleviating continuous cropping obstacle was clarified through different root separation ways, and the differences and synergies of heterologous double-root in alleviating continuous cropping obstacle were discussed. Compared with non-rhizosphere soil, the seedling quality index and plant biomass of heterologous double-root coffee or homologous double-root coffee decreased significantly after culturing in rhizosphere soil. After non-rhizosphere soil culture, there were no significant differences in the seedling quality index or plant biomass between heterologous double-root coffee and homologous double-root coffee. The seedling quality index, root biomass of C. liberica and C. canephora, and total plant biomass of heterologous double-root coffee were significantly higher than those of homogenous double-root coffee after rhizosphere soil culture. Continuous cropping obstacle inhibited the growth of coffee, but had more effect on homologous double-root coffee. Heterogenous double-root coffee alleviated the growth obstacle of continuous-cropping coffee by C. liberica roots. The seedlings quality of the heterologous double-root coffee separated root by nylon net was better than that of root undivided or separated root by double pot under continuous cropping, and the root growth of C. canephora was the best in nylon net separation. Root allelochemicals of C. liberica promoted the root growth of C. canephora. There was no significant difference in the seedlings quality of heterologous double-root coffee between root undivided and separated root by double pot, and the C. liberica root growth of root undivided was worse than that of double pot separation. The root growth of C. canephora inhibited the root growth of C. liberica when the heterologous double-root were in contact with each other, but this inhibition was not related to the allelopathic substances in the C. canephora rhizosphere. The root growth of C. liberica had no significant difference in nylon net separation and double pot separation. There was no effect on the root growth of C. liberica with or without the allelopathic substances. of C. canephora. The root system of C. liberica alleviated the continuous cropping obstacle by reducing the inhibition of allelopathic environment and promoting the root growth of C. canephora by its allelopathic substances. The results would provide a theoretical basis for the application of heterologous double-root grafting in the field.