The Asian champions, 3-0 winners over Oman at the weekend, face fierce rivals Australia away on Tuesday and warned they can still improve after back-to-back blowouts in Saitama.
"It was important to go into the Australia game in good shape," Honda said. "We have to keep this run going but we can still play better."
Ryoichi Maeda put Japan ahead with a looping header in the 18th minute, before Honda quickly doubled the home side's lead, finishing in style after a clever ball from Yasuhito Endo.
Jordan forward Abdallah Deeb was then sent off after receiving his second yellow inside two minutes for leaving Japan captain Makoto Hasebe with a cut head from a stray elbow.
Japan took advantage, Honda tapping in his second on the half hour and Shinji Kagawa squeezing in a fourth in the 35th minute after more horror defending from Jordan.
Honda, who also found the net against Oman, completed his hat-trick in the 53rd minute from the penalty spot before being replaced to conserve his energy for the Socceroos.
Substitute Yuzo Kurihara headed Japan's sixth a minute before time to further boost their goal difference and hand Jordan a record-equalising loss.
Honda, who had immediately called "I'm taking it" after Maeda had been tripped for the penalty, played down his treble.
"They let me take the penalty," the bleached-blond midfielder deadpanned. "It was an easy hat-trick with the great passes I got and then the penalty."
Hasebe also said Japan would need to step up against Australia, who they beat in last year's Asian Cup final.
"We scored goals at right time again so we were able to control the pace of the game," he said. "We can still raise the tempo and need to change gears quicker.
"Our pace dropped in the second half so we will have to keep our foot down against Australia."
Jordan drew their opening Group B game 1-1 with Iraq, currently under the stewardship of former Japan coach Zico.
Oman were hosting Australia later on Friday.