The invention discloses an alfalfa drought tolerance identification method, comprising the following steps: after sterilization on seeds, carrying out a conventional sprouting experiment, after a seedling has 3-4 main leaves, performing thinning and final singling, reserving materials whose plant size and height are roughly consistent, and carrying out a water controlling experiment in a greenhouse; in the 8th-11th day, taking the plants out to count the number of roots of each plant of alfalfa, including the number of main roots, lateral roots, and fibrils on the lateral roots; after processing for 20 d, respectively measuring seedling height, fresh weight of root systems, dry weight of root systems, leaf chlorophyll contents, stomatal conductance, leaf free water content, leaf surface bound water content, proline content and root volume of each processing group; performing data reduction, calculating average values, and calculating a drought tolerance coefficients and a comprehensive drought tolerance value of each variety; and determining salt tolerance of the varieties according to the comprehensive drought tolerance value. The method performs multivariate statistical analysis on agronomical characters and indexes of an alfalfa seedling stage, so as to perform comprehensive judgement and evaluation on the drought tolerance of alfalfa.