This study experimentally investigates the effect of a bumpy base on the Brazil-nut phenomenon in a vertically vibrated granular bed. The rise dynamics of an intruder is determined by the particle tracking method. The results indicate that the rise time increases with an increase in the base roughness, and the variation of the rise time with different base factors is more pronounced with smaller vibration acceleration and higher vibration frequency. A theoretical model is employed to measure the penetration length of the intruder and the drag force between the intruder and the immersed beads. The penetration length is reduced and the drag force is enhanced with surface roughness of the base. Additionally, the transport properties of the vibrated glass beads are also measured and discussed. With greater base roughness, the strength of the diffusive and convective motion is reduced leading to a weaker Brazil-nut effect.