We present in this paper a DEM study on the segregation behavior of vibrated binary mixture, by focusing on the influence of vibration modes. The numerical simulation program includes a number of vibration tests on a binary mixture in a cylindrical bed, which are performed under different vibration velocity modes, frequencies and amplitudes. We utilize a novel segregation index, namely, the graphic segregation index (GPSI), to characterize the segregation behavior and trace the segregation evolution for binary mixtures. The numerical simulations reveal that the influence of velocity mode is coupled with that resulting from vibration frequency. The binary mixture tends to segregate at a low frequency, with little influence exerted by the velocity mode, whereas it does not fulfill complete segregation at a relatively high frequency, with the vibration frequency having some limited impact on the segregation behavior. Given an intermediate frequency the segregation behavior of the mixture is a little mixed for various velocity modes. It is also found that increasing vibration amplitude enhances the segregation degree of binary mixture. The operation of percolation mechanism in the broad sense is assumed to be primarily responsible for the occurrence of segregation in this study, and this alleged percolation mechanism, as an overall effect, is a result of three effects: the random gap effect, the size-and-mass dependent acceleration and the intrusion and expulsion effect.