Two stubbles (rotation stubble and continuous cropping stubble) and six plant materials (Codonopsis pilosula, Allium stativum, Zea mays, Astragalus mongholicus, Sophora flavescens and Helianthas annuus) were selected to form six planting modes of Codonopsis pilosula monoculture and intercropping, and a field random block test of two factors of the stubble and the intercropping mode was set up. The alleviation effect of different stubbles and intercropping crops on continuous cropping obstacle of C. pilosula was measured by monitoring the changes of growth indexes (vine length, main root length, main root diameter, fresh and dry weight of the underground part), root yield and quality indexes (root polysaccharide content, alkynin content, alcoholsoluble extract content and ash content) of the roots. The results showed that: (1) the effects of single cropping and intercropping on the growth, quality and yield of C. pilosula under rotation are more obvious than those ander continuous corpping, and the effects of intercropping under two stubbles are more obvious than those under single cropping. (2) The intercropping treatment with H. annuus, A. stativum and Z. mays had more significant effects on the main root length, the main root diameter and the fresh and dry weight of underground part of C. pilosula than C. pilosula monoculture and other intercropping treatments (intercropping with A. mongholicus and S. flavescens); (3) The intercropping treatment of A. stativum and H. annuus could significantly increase the root yield of C. pilosula during two seasons. Especially, A. stativum performed best. The crop rotation and continuous cropping C. pilosula intercropped with A. stativum increased the yield by 49.92% and 22.55% respectively as compared with the control; (4) Intercropping with A. stativum could effectively increase the polysaccharide content, alkynin content and alcoholsoluble extract content in the roots of C. pilosula during two seasons. The effect of C. pilosula monoculture and other intercropping treatments on the quality improvement of C. pilosula during two seasons was not as good as that for A. stativum intercropping. The study found that, based on the comprehensive analysis of the growth status, root yield and quality of C. pilosula, the participation of the party in A. stativum intercropping was the most beneficial for the plant growth of C. pilosula under two crop rotation, which could effectively alleviate the continuous cropping obstacle of C. pilosula and significantly improve the yield and quality of its medicinal parts. Moreover, the enhance effect under crop rotation was more significant than that under continuous cropping.