A field experiment was conducted to evaluate the effects of bio-organic fertilizer and microbial agent on the growth of tea chrysanthemum and soil fertility under continuous cropping cultivation system. Taking Beijing tea chrysanthemum as experimental plant material，treatments under conventional fertilizer(CK)，bio-organic fertilizer(T1)，microbial agent(T2)，and bio-organic fertilizer combined with microbial agent(T3)were designed.Results showed that the application of bio-organic fertilizer and microbial agent significantly increased the contents of soil organic matter，total nitrogen，available nitrogen，available phosphorus，available potassium，and the amounts of soil bacteria，fungi and actinomycetes，and improved the survival rate，plant height，crown diameter，branches，yield，total flavonoid and chlorogenic acid content of tea chrysanthemum. Treatment of T3 had the best effect under the experimental conditions. Compared with CK，the average contents of soil organic matter，total nitrogen，available nitrogen，available phosphorus，available potassium，the amounts of bacteria，fungi and actinomycetes，the survival rate，yield，total flavonoid and chlorogenic acid content of tea chrysanthemum were significantly increased by 20.18%，10.06%，10.28%，12.22%，33.17%，96.03%，40.56%，69.06%，41.55%，60.74%，42.59% and 33.38%，respectively. In conclusion，the application of bio-organic fertilizer and microbial agent could improve soil fertility and microbial community structure，increase the efficiency of nutrition supply，significantly promote the growth，increase the yield and improve the quality of tea chrysanthemum，and play a positive role in alleviating the obstacles of continuous cropping. The results could provide a reference for the prevention and control of continuous cropping obstacles of tea chrysanthemum in the mountainous area of Beijing.