Variation of rhizosphere and non-rhizosphere cultured soil microbes at the different growth stages of Fritillaria pallidiflora were analysed. The correlation of rhizosphere soil microbes with imperialine content were discussed. The results showed that the ecological distribution characteristics of rhizosphere and non-rhizosphere soil microbes at every growth stages (Re-greening stage, bud stage, full flowering stage and harvest-time) of Fritillaria pallidiflora were all bacteria > actinomycete > fungi. Only in bud stage, non-rhizosphere fungi number is more than rhizosphere’s. At other stages rhizosphere bacteria, actinomycete and fungi were more than non-rhizosphere’s. Especially, for bacteria, the rhizosphere effect of Fritillaria pallidiflora was obvious. Number of bacteria and fungi in the rhizosphere soil of full flowering stage are most in all stages. Soil fungi number had extremely marked positive correlation with imperialine content.