A source told the new issue of Us Weekly: "Tom said absolutely no way and thought going backward would be bad."
Holmes starred as girl-next-door Joey Potter on Dawson's Creek for six seasons and, in a November 2011 appearance on Good Morning America, said a reunion movie "would be fun. I had so much fun working on that show and I loved everyone so much and I think about it with such fond memories".
Holmes filed for divorce in New York City on 28 June after five years of marriage to Cruise and is now said to be planning a return to the acting world.
She just wrapped a modern version of Chekov's The Seagull and is at work on Molly, which she co-wrote and produced. Jack and Jill, in which she stars alongside Adam Sandler, went on DVD release this week.
Meanwhile, Cruise - one of the world's most enduring film stars - turned 50 on Tuesday.
He's been sensibly bunkered down in Iceland, filming his latest sci-fi adventure, Oblivion, however US Weekly reports he boarded a private jet at 2 am on his birthday at the Reykjavik airport in Iceland, to head to California.