Ngannou faces AJ on March 8 in Saudi Arabia having made his professional boxing debut in October against Tyson Fury.
The Cameroonian made a switch to boxing after walking out on the UFC and the offer of a $10million (£8m) payday to fight Jones.
He instead signed for the Professional Fighters League, who gave Ngannou the freedom he always wanted to box at the same time.
Jones joined the heavyweight cageside in Riyadh for the PFL vs Bellator event and he was probed on the boxing bout with AJ.
And Jones replied: “I’m rooting for Francis to win, only because his story, how far he’s come in life and being a fellow mixed martial artist.
“So I’m rooting for Francis but Anthony Joshua, he’s being doing this since he was a young boy and I’m the type of guy who just gives respect where it’s due.
“So if I was to put my money on it – not that I gamble – I would put it on Anthony Joshua but I am rooting for Francis.”
Ngannou, 37, astonishingly dropped Fury, 35, but still suffered a controversial split-decision loss.
Although the performance was enough to bring Joshua, 34, to the table for another huge crossover clash in the desert.
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Meanwhile Jones, 36, is coming off a chest injury that forced him out of his UFC title fight against Stipe Miocic, 41, in November.
He has since been called out by interim champ and British star Tom Aspinall, 30, while the PFL are open to a cross-promotion to fight Ngannou.
But Jones diplomatically said: “I feel like there’s a lot of fights that the world wants right now.
“The Tom Aspinall fight is still really massive, Francis Ngannou and I would be really massive.
“And Stipe, to the hardcore fans, it’s still a respectable opponent. I don’t know how the cards are gonna fall.
“My prediction is I would beat Stipe Miocic, my prediction is I would beat Tom Aspinall and Francis Ngannou.
“The way it unfolds is really not of my business my job is just to always do what I’ve done from day one.”