The control effect of two strains (F05 and 30371) on seedling blight and root rust rot disease of P. quinquefolium was optimized by uniform design. The results showed that when sow the P. quinquefolium seed only applying strain 30371 with 1.6×109/m2 for 5 times and planted P. quinquefolium root applying strains F05 and 30371 for one time at amounts of 6.984×108/m2 and 1.6×109/m2 respectively. The control efficiency against seedling blight was 46% in greenhouse, and the root rot disease control efficiencies were 88.93% and 44.57% respectively in greenhouse and field, the root weight of Panax quinquefolium in greenhouse treated with F05 and 30371 increased 22.4% compared to the control plants. The combination of F05 and 30371 could decrease disease incidence in ginseng plants and enhance plant growth.