Abscisic acid (ABA) is a vital stress resistant hormone of plant in coping with adverse environmental conditions, such as drought stress. Sensitivity of seed germination to exogenous ABA treatment could link to different drought tolerance ability of different plant species. Here, we selected alfalfa seedlings (S0-50) from seeds germinated under 50 μM ABA treatment. The S0-50 plant showed more sensitivity in stomatal closure to exogenous ABA and PEG treatments, and also stronger drought tolerance than the plant of ABA-sensitive seed during germination (S0-0). Testing of ABA content in leaf indicated that the S0-50 had a higher ABA content in normal and under drought stress growth conditions than that of the S0-0 plants. The seed of S0-50 next generation (S1-50) showed significantly higher germination ratio under 50 μM ABA treatment, and also had longer root after 15% PEG6000 treatment than the segregated ABA-sensitive seed (S1-0). We found a cytosol-nucleus dual-localized PPR protein gene MsSOAR1 was significantly highly expressed in S0-50 than in S0-0 plant. Overexpression of AtSOAR1, a negative regulator in ABA-mediated Arabidopsis seed germination inhibition, and also a homologous gene of MsSOAR1, significantly improved alfalfa drought tolerance, branch number and plant height, and reduced the expression level of ABA receptors MsPYL5 and MsPYL6. The results suggest that ABA-insensitive during seed germination could associate with repression of ABA signaling transduction. Selection of alfalfa seedling during seed germination with exogenous ABA could be a way to obtain drought tolerance germplasm, at least in ‘Zhongmu No.1’ alfalfa cultivar the plant material we used in the experiment.