The field sequential modulation of a Nd:YVO4/MgO:PPLN intra-cavity, frequency doubling green laser was studied. The modulation frequency was set at 1 kHz and the duty cycle was changed from 20% to CW operation. It was shown that the quasi-phase matched (QPM) temperature decreases with an increase of the modulation duty cycle, and in turn causing the peak efficiency to rise. It was found that the temperature change in MgO:PPLN and the thermal lens effect in Nd:YVO4 crystal were the respective origins of these observed experimental phenomena.