Experiments have been performed to investigate the effect of subharmonic motion on size segregation in vertically vibrated granular beds. In our experimental systems, symmetric normal convection of granular particles is induced when vibration acceleration is sufficiently large, and subharmonic motion of the particles appears when vibration acceleration is above another larger critical value. Observations reveal that particle convection is the main mechanism leading to the segregation of larger intruder particles imbedded in smaller ones, the convection flux dominates the rising time of the intruder, and a distinct retardation of the segregation time is induced when the bed’s bulk motion undergoes period-doubling and period-quadrupling bifurcations. An analysis of the convection due to the effects of air is given. Then the mechanism leading to such retardation is discussed and simple expression for the segregation time is formulated. The obtained results agree well with experimental values.