In this paper, we study the gravitational waves of holographic QCD phase transition with hyperscaling violation. We consider an Einstein-Maxwell Dilaton background and discuss the confinement-deconfinement phase transition between thermally charged AdS and AdS black holes. We find that hyperscaling violation reduces the phase transition temperature. In a further study, we discuss the effect of hyperscaling violation on the GW spectrum. We found that the hyperscaling violation exponent suppresses the peak frequency of the total GW spectrum. Moreover, the results of the GW spectrum may be detect...