The invention discloses an efficient cultivation method of intercropping flue-cured tobacco and soybeans. The efficient cultivation method includes the following steps that (1) base fertilizer is applied in furrows before ridging in a tobacco field; (2) soil preparation and ridging are carried out on the tobacco field in good time; (3) the whole ridges are covered with a mulching film; (4) two rows of shaft well type transplanting holes are formed in the two sides of each ridge top, and two rows of crop planting holes are formed in the zone between the two rows of shaft well type transplanting holes; (5) flue-cured tobacco is transplanted in a shaft well mode, and tobacco plant transplanting position is located over the base fertilizer applied in furrows; (6) while the flue-cured tobacco is transplanted, soybeans are sown in a dibbled mode in the two rows of crop planting holes; (7) the flue-cured tobacco and the soybeans are managed through the normal method in the following steps. The influence on flue-cured tobacco growth by spring drought in the southwest region, the nicotine content of the flue-cured tobacco on the upper portion is reduced remarkably, the potassium content of the flue-cured tobacco on the upper portion is obviously increased, richness and diversity of rhizosphere soil bacterial communities of the tobacco plants are remarkably improved, flue-cured tobacco successive cropping obstacle is overcome, the income of peasants is increased additionally, and the efficient cultivation method is particularly suitable for the southwest region in China.