The investigative results of modulated pulse output from an LD end-pumped passively Q-switched intracavity-frequency-doubling Nd:YVO4/KTP laser with Cr4+:YAG saturable absorber are presented. The numerical stimulations of these modulated pulses are carried out basing on the rate equations. It indicated that the modulations are attribute to the frequency beating of two eigenstates of the resonant polarized modes. The theoretical calculations are in good agreement with the experimental observations.