Treating the two-year-old Panax notoginseng by 4 water irrigation settings, conventional irrigation and 3 kinds of water deficit irrigation (irrigation to 60%, 50%, 40% of field capacity), we studied the effects of different water treatments on the soil microenvironment and the growth of Panax notoginseng in the vegetative growth stage. The results showed that in the mild water deficit (irrigation to 60% of the field capacity), the leaf length, leaf width, petiole length and cut length of Panax notoginseng gained a high level. For the soil microorganisms, bacteria accounted for the largest proportion of microbial colonies in each treatment. The maximum trend was the same as the total soil microbial count. With the increase of water deficit, the number of fungal colonies increased first and then decreased, and the number of actinomycetes and bacterial colonies showed a decreasing trend. Soil enzyme activity showed a trend of increasing first and then decreasing. With the 50% of the field capacity, the urease activity got the maximum, 0.15 mg/(g?d). With the 60% of the field capacity, the catalase and acid phosphatase activities were the highest, 3.57 mL/g and 439.5 μg/(g?d) respectively. The number of actinomycetes and bacteria colonies and acid phosphatase activity in soil were significantly correlated with the increment of the plant height, petiole length, leaf length, leaf width and cuts length of Panax notoginseng(P<0.01). It can be concluded that the 60% of the field capacity was the best solution in the greenhouse cultivation in the vegetative growth stage in this study.