Soil phosphorus (P) deficiency is one of the main factors that diminish the yield of crops on the Loess Plateau. Fagopyrum tataricum is a dominant cereal plant on the Loess Plateau, whose responses to low-P stress are significantly different and dependent on its genotypes. Therefore, screening genotypes with efficient P utilization is an important approach to increase the yield of F. tataricum and promote the sustainable development of local agriculture. With fourteen F. tataricum genotypes, the agronomic traits, physiology and biochemical characters of F. tataricum at seedling stage under normal (2 mmol·L-1) and low-P treatment (0.2 mmol·L-1) were studied by using sand culture. By examining the characters of selected F. tataricum at seedling stage, the varieties of F. tataricum with low-P tolerance were screened out and their evaluation indices were assessed to provide theoretical basis for the breeding of F. tataricum with high P-efficiency and the infertile soil cultivation on the Loess Plateau. The results showed that under low-P stress, the shoots of all genotypes were more affected than roots, with the decline of shoot aboveground index, average root diameter, root surface area and root volume, whereas the length of main root was elongated. Root activity and soluble protein content were decreased. In contrast, other physiological and biochemical indicators were increased. Moreover, plant total phosphorus content and plant phosphorus accumulation reduced, but phosphorus use efficiency increased. The principal component analysis divided the 22 individual indicators into four mutually independent comprehensive indicators (cumulative contribution rate of 90.1%). Cluster analysis divided 14 kinds of F. tataricum into three categories: Low phosphorus tolerant, intermediate and phosphorus sensitive. In order to investigate the index of low-P tolerance of F. tataricum at seedling stage, the optimal regression equation was established with the comprehensive evaluation value of low-P tolerance (D value) as the dependent variable and the low-P tolerance index of each indicator as the independent variables. Seven indicators of root surface area, root length, plant height, aboveground dry mass, acid phosphatase, phosphorus accumulation and POD activity were examined, which could be used for the rapid identification of low-P tolerance of F. tataricum at seedling stage.