The purpose of this paper is to explore the effects of acid treatment on root morphology and architecture in seedlings of Malus hupehensis var. pingyiensis. The rootstock seedlings were cultured in 1/2 Hoagland nutrient solutions of different pH (pH 4, pH 4.5, pH 5 and pH 6), respectively. The parameters of root architecture were measured in the day 4, 8 and 12 with the professional WinRHIZO 2007. Compared with the control (pH 6), the treatments significantly decreased the fractal dimension, length, diameter, surface area and volume of roots in day 8 and 12, and they kept decreasing followed the increase of the acidity and treatment time. The growth of lateral roots was more susceptible to acid treatment than taproots. In addition, the acid treatment mainly inhibited the growth of rootlets, significantly decreased the proportion of rootlets that changed the composition of roots, and then simplified the space structure of roots.