Abstract: In this research, field experiment was conducted to explore the economic effect and ecological benefit of reducing chemical fertilizer rate with autochthonous propagation agent application in tobacco production. The conventional fertilizer application was set as the control in flue-cured tobacco production area of Yishui district, Shandong Province. On the basis of not changing the NPK proportion of the original fertilizer, the proportion of 0%, 15% and 30% of NPK contents were reduced in combination with adding the autochthonous propagation agent as microbial components. The effects of flue-cured tobacco yield and quality, microbial quantity in rhizosphere soil and field fertilizer leaching loss rate were studied. The results showed that the treatments with autochthonous propagation agent application would not hinder the growth of flue-cured tobacco and were beneficial to economic character, chemical composition, and sensory evaluation quality of tobacco leaves. In addition the treatment increased the functional microbial diversity and changed the microbial community structure in rhizosphere soil, reduced the leaching loss rate of fertilizer in the field, and finally increased the fertilizer use efficiency. In conclusion, the fertilization method of autochthonous propagation agent in combination with a 30% proportional reduction of NPK chemical fertilizer is practicable, and can achieve better economic and ecological benefits.