Abstract: 【Objectives】Root system is particularly important for the nutrient and water uptake of fruit trees. Few researches are reported on the root architecture and spatial distribution related to nutrition because of the hugeness and complex of root distribution. In this research, Epson digital scanner and plasma atomic emission spectroscopy were used to study the two-dimensional architecture and nutrient concentration of plant roots, to explore the effects of nutrient deficiency on root morphology and the relationship with plant nutrient uptake.【Methods】A sand culture pot experiment was conducted and the seedlings of Poncirus trifoliata were grown as test materials. Root samples were scanned with an Epson digital scanner (Expression 10000XL 10, Epson Inc. Japan) and the data were analyzed with the WinRhizo Pro (S) v. 2004b software (Regent Instruments Inc., Canada) to obtain the root length, root volume and root surface area. The concentrations of nutrients were determined by inductively coupled plasma atomic emission spectroscopy (Thermo Inc, IRIS Advan, United States).【Results】The total root length, surface areas and volumes are reduced significantly in the nutrient deficiency media. When the root system was classified into fine, middle and coarse roots according to their diameters, the effects of nutrient deficiencies on the three fractions were different with treatments. Compared with the control, the root length, surface area and volume of fine and coarse roots are reduced, but the surface area and volume of middle roots are increased remarkably under P deficiency; the root length, surface area and volume of fine and middle roots are reduced under K and Ca deficiency. The nutrient deficiencies induce significant decreases of shoot and root biomass, stronger inhibition effect on shoot than on root under the P deficiency, but opposite effect under K deficiency, least effect under Ca deficiency. The Zn concentrations of plants are significantly increased under three nutrient deficiency media, the Fe concentration increased under the Ca deficiency but decreased under the K deficiency, Ca concentrations increased under the P and K deficiencies but decreased under the Ca deficiency.【Conclusions】The nutrient deficiencies lead to worse root morphology, as a concequence, decreases the absorption of nutrients in different extents and the growth of plant root and shoot, and leads to the peculiar symptoms corresponding to the different nutrient deficiency environment.