The Blades defeated Charlton on Sunday to book an FA Cup semi-final date with Hull City, with Flynn grabbing their first goal in a 2-0 win.
The League 1 side were deep in the relegation mire at the beginning of February, but Clough has since guided his side to nine successive victories and they are now preparing for a trip to Wembley.
Flynn told Sky Sports News: "It's been unreal. We're really looking forward to it. We went to Wembley two years ago in the play-off final and it didn't end so well. It'll be a great occasion.
"The manager has galvanised the squad. There's a real team spirit. He's been great for us and the performances have shown that. We've deserved the nine victories that we've had.
"February was a low point in the season but we've turned it around. We've recorded nine victories on the bounce, with eight clean sheets. We're definitely on the up."
United's good run of form has taken them to within 11 points of the play-off places but Flynn feels that could be a step too far this season.
The 25-year-old said: "We've got ourselves out of the relegation zone and things are going well, but I think we have to consolidate that and make sure we keep our League 1 status.
"There are a lot of games to go and plenty of points to play for. We'll keep taking one game at a time and see where that leads us."
The performances of defender Harry Maguire have reportedly attracted the attention of Premier League sides such as Liverpool and Chelsea, and Flynn says the interest in his Bramall Lane team-mate is well deserved.
"Being linked to those clubs is just reward for how he's been playing," said Flynn.
"He showed how good he is when he played against Christian Benteke at Villa Park, and he continues to do that week-in week-out. I'm not surprised by the speculation."