Plant roots are important organs that function in the uptake of water and nutrients from the surrounding soil, and the physiological and morphological traits of roots affect shoot growth. Therefore, the present study assessed the effect of air root pruning for 10, 30, or 50 d on the biomass allocation, root morphology, and root absorption area of juvenile-stage Platycladus orientalis seedlings, with intact plants used as controls. The results indicated that (1) root biomass, aboveground biomass, total biomass, root length, root surface area, root volume, and root tip number all increased with air root pruning time. In addition, the total and active absorption areas of the roots significantly increased. (2) Air root pruning significantly affected the biomass allocation pattern of P. orientalis seedlings, and the root:shoot ratio initially increased but then decreased, whereas it only decreased in the control. (3) The diameters of most of the P. orientalis roots were ≤ 0.5 mm. Furthermore, air root pruning improved the length, surface area, volume, and tip number of ≤ 0.5 mm roots, when compared to the control, and the roots of this diameter range accounted for 79% of the total root tip number. (4) The biomass and root characteristics of the P. orientalis seedlings were closely related. In addition to the average root diameter, the aboveground, root, and total biomasses of the pruned seedlings were positively correlated to root length, surface area, volume, and tip number. However, the root:shoot ratio and aboveground biomass were negatively correlated. Consequently, air root pruning technology could be used to dramatically promote the growth and survival of P. orientalis seedlings by improving their root morphology and enhancing the absorption area of their roots during early growing stages.