Under the condition [0mmol/L(P),raise in vermiculite] of phosphorus stress, variation in root morphology and biomass among different soybean genotypes at seedling stage were studied, the result shows: At two-leaf age, higher P-efficiency genotypes(K1 and K2) don’t develop their potential advantages; at four-leaf age, some characteristics of K1 and K2, such as lateral root number, lateral root length, root absorbent area and dry weight of shoot are all less reduced than those of intermediate P-efficiency genotypes(Z1 and Z2) and of lower P-efficiency genotypes(M1 and M2), and dry weight of root and R/S of higher P-efficiency genotypes are more increased than those of the others. The comprehensive evaluation indicates that comprehensive value (comprehensive index of evaluating characteristics of P-efficiency) of K1 and K2 are both larger significantly than those of Z1 and Z2 and of M1 and M2, it shows that K1 and K2 have stronger capability of tolerance to P deficiency than the other genotypes. But it is not true that all characteristics of higher P-efficiency genotypes have an advantage over intermediate P-efficiency and lower P-efficiency genotypes; root surface area and active absorption area can be used to evaluate characteristics of P efficiency, and four-leaf age is the right age to screen soybean genotypes with tolerance to P deficiency.