Flynn, who was appointed after Newport sacked boss Graham Westley, has won both his games in charge.
And the morning after Tuesday's victory at Morecambe, the Welshman received a congratulatory text message from former Arsenal striker Henry, with whom he has been qualifying as a coach.
"It was surreal," said Flynn.
"He's one of my heroes in the game. He's just pure class and he's like that off the pitch as well.
"I asked him to put his boots back on but he wasn't so forthcoming!
"For a football fan, which I am, it was unbelievable, and something which made me smile on Wednesday morning when I had my little boy waking me up at 6.30 in the morning, after getting back from the game at 4am."
Newport moved off the foot of the League Two table and are now seven points from safety after beating Morecambe.
County were bottom and 11 points adrift when they sacked Westley but have won their two games under Flynn.
The 36-year-old former Newport midfielder has been studying for his coaching badges with the Football Association of Wales, under the tutelage of Wales assistant manager Osian Roberts.
Former Barcelona and France forward Henry has been on the same course, and watched Wales' rugby team train earlier this month.
Now a television pundit as well as Belgium's assistant manager, Henry has told Flynn he can call him for advice whenever he needs it.
"It's just nice to see that support," added Flynn, whose Newport side host Blackpool on Saturday.
"Learning from people like that - Patrick Vieira, David Ginola, Sol Campbell - it's a great mix of people.
"It's all put together by Osian and Lennie Lawrence, and it's attracting the right calibre of manager. Picking their brains and seeing how they work is invaluable."
Newport County caretaker manager Mike Flynn has revealed how Thierry Henry has lent his support to the Exiles' bid for League Two survival.