As a major abiotic stress, drought causes instability and deterioration of malt barley quality. There is distinct difference among barley cultivars in the responses of the main malt quality traits to drought stress. In the previous study, we identified some Tibetan wild barley accessions with relatively less change of malt quality traits under drought. In this study, we examined the impact of drought stress during grain filling stage on grain weight and several important malt quality traits, including total protein content, β-glucan content, limit dextrinase activity, β-amylase activity, and protein fractions in four barley genotypes (two Tibetan wild accessions and two cultivars). Drought treatment reduced grain weight, β-glucan content, and increased total protein content, β-amylase activity. These changes differed among barley genotypes and treatments, and are closely associated with grain filling process and kernel weight. All the results indicated Tibetan wild barley had great potential for developing drought tolerant barley cultivars. Relatively stable kernel weight or filling process under water stress should be highlighted in malt barley breeding in order to reduce the effect of water stress on malt barley quality.