The field experiment was conducted to investigate the effects of tobacco garlic crop rotation and tobacco garlic crop intercropping on the bacteria, fungi, actinomycetes, potassium bacteria and phosphate solubilizing bacteria in rhizosphere soil and bulk soil at different mature stages in different years, and tobacco monoculture treatment was used as control. Results showed that, the numbers of bacteria in rhizosphere soil for the tobacco garlic crop rotation and intercropping treatment were greater than that of tobacco monoculture and this was more evident with increasing in growth period. The bacteria numbers in rhizosphere soil for tobacco garlic crop rotation and intercropping treatment were 1.41 and 1.24 times that of tobacco monoculture in 2014. The rhizosphere soil had the fewest fungi number for tobacco garlic crop rotation treatment at mature stage of middle leaf and upper leaf. But fungi number in non-rhizosphere soil for the tobacco garlic crop rotation and intercropping treatment were higher than that of tobacco monoculture. The actinomycetes number in rhizosphere soil for the tobacco garlic crop rotation and intercropping treatment were 2.01 and 2.93 times in 2013, and 1.12 and 1.28 times that of tobacco monoculture treatment in 2014. The numbers of the potassium bacteria and phosphate solubilizing bacteria in rhizosphere soil for the tobacco garlic crop rotation and intercropping treatment were significantly higher than that of tobacco monoculture from intermediate to final growth period, and the same trend was observed for phosphate solubilizing bacteria in non-rhizosphere soil. The tobacco yield and ratio of the middle and superior classes of tobacco leaves for tobacco garlic crop rotation and intercropping treatment were significantly higher than that of tobacco monoculture treatment in different years. The systems of tobacco garlic crop rotation and intercropping can improve the microbial structure and quality of the rhizosphere soil.