The 22-year-old, who has 17 caps for Wales and played four matches at Euro 2016, has made just one league appearance for the Eagles since Pardew took over at the start of 2015.
"Jonny and I just can't seem to come together. In pre-season he's fit and then gets injured again. It was a terrible tackle at Farnborough," Pardew told the Croydon Advertiser.
"We were at deadline day last month and I'm looking at my numbers and thinking I can't see Jonny getting a game.
"Really and truly, with the amount of time he's got, I can't keep him here and have him as a substitute.
"I know our fans love him, and again, he may have influenced the game at certain points as a sub more than others or he might have got himself up to speed. He might have.
"We have almost had a discussion in that does Jonny need a new environment? Does he need a new start? It just seems to not be working here."