The 25-year-old all-rounder cracked a match-winning 70 off just 47 balls in the second one-day international against Bangladesh.
He struck nine fours and four sixes in his 10th one-day half-century, second in a row following his explosive half-century and four-wicket haul in the first match at Chittagong last week.
"I keep saying he's an important part to this one-day side, very important," Vaughan said.
"The key thing about Andrew is the way he practices. Over the last nine months that he's been in this rich vein of form, his progression has become evident and it's because of the way he practices.
"He's focusing on specific things in his batting and if he continues to do that, he'll score a lot more runs."
Flintoff, who made a slow start in international cricket because of a back problem and weight gain, was named man of the series in England's triangular series triumph against Pakistan and South Africa earlier this year.
He also shone in a Test series against South Africa in the English summer, scoring a fighting century at Lord's and a fiery 95 at The Oval.
"He's hitting the ball in areas where there aren't any fielders. When he came in, the ball was doing a bit under the lights, but he settled the issue in no time," Vaughan said.
England restricted Bangladesh to a meagre 134 for nine from their 50 overs but were in trouble at 37 for four before Flintoff dominated in a 100-run stand with Vaughan to see the visitors through with 22 overs to spare.
Vaughan, however, was disappointed that Bangladesh managed to play out the full 50 overs after tottering at seven for four.
"We had them at seven for four and then they got 130, so you could say we allowed them to get too many runs," he said.
"I'm being very harsh here, but I didn't think we were very good in the field. Our goal is to be the best fielding side in the world and I can say we were not our best today."
But the skipper said the performance did not mean England were not professional enough.
"The killer instinct is definitely there," he said. "We've just beaten a team in about 25 overs after we contained them to 130, that's a good achievement."
