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."

Scientists have analysed a cell found in heart scar tissue which could cause increased risk of cardiac arrest.
Myofibroblasts cells in patients might increase the likelihood of an electrical "short circuit".
"Cells recruited to the heart to repair damaged tissue might also be the cause of post-attack arrhythmia," said Prof Chris George.
The university's molecular cardiology team has led an international team of experts in the research funded by the British Heart Foundation which has also found myofibroblasts can cause irregular heart rhythms which can lead to sudden death in post-attack patients.
In Wales, around 50,000 people alive today have survived a heart attack and the latest findings could lead to an improved diagnosis for victims and better treatments.
"The number of myofibroblasts that infiltrate into damaged areas of the heart is quite amazing," said Prof George.
"To be able to also show that there's a link between the number of these myofibroblasts and the onset of arrhythmia lays the foundations for developing new approaches to prevent post-heart attack rhythm problems in patients."
Ruth Coombs, head of BHF Cymru, added: "By investing in research in Wales today, we're making tomorrow's tests and treatments for heart conditions possible."

Jamieson, who lost his place to on-loan Rangers 20-year-old Liam Kelly, had been sent out on loan to junior outfit Bo'ness United earlier this month.
He would become Accies' third goalkeeping addition of the summer.
Gary Woods was signed permanently from Leyton Orient and Remi Matthews on loan from Norwich City.
The Premiership club lost Michael McGovern to Norwich this summer after his Euro 2016 displays for Northern Ireland.
Meanwhile, 16-year-old Jon McCracken followed him from New Douglas Park to Carrow Road earlier this month.
Jamieson had made 101 appearances for Livingston, 16 while they were in the Championship last season.

Mexico City Mayor Miguel Ã
Newport County caretaker manager Mike Flynn has revealed how Thierry Henry has lent his support to the Exiles' bid for League Two survival.
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Research at Swansea University could help predict further attacks and detect problems in heart attack patients.
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Goalkeeper Darren Jamieson has been released by Livingston, with the League One club saying that the 25-year-old is to join Hamilton Academical.
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Parts of Mexico City's historic centre have been closed to traffic as film crews shoot scenes for a new Godzilla film in the Mexican capital.