In view of the new generation HF 3GALE signal applied in US Army to multiple data encoding on communication link layer to improve the transmission reliability of its protocol information, a modified pulse jamming method is proposed against such multiple data encoding. Firstly, a jamming model affected on the periodic pulse signal which can be in advance scrambled by public pseudo random scrambling sequence is built up. Then, on the basis of formula derivation for signal receiving and processing, the impacts on jamming performance are analyzed from some jamming parameters such as pulse duty ratio and pulse period, along with other parameters such as scrambling sequence's missynchronization and jamming frequency offset. Finally, this jamming method is carried on simulation experiment, resulting in some relevant conclusions. The experiment results prove the effectiveness of the modified pulse jamming against the reliable transmission of 3GALE signal protocol information. The jamming effect is the best when the pulse duty ratio is set 75% and the pulse period is set to make pulse duration equal to integer multiple symbol time length TB. The decline of jamming effect resulting from scrambling sequence's missynchronization within 2TB or jamming frequency offset within 80 Hz, can be improved fairly by increasing the jamming-to-signal power ratio.