A source told Us Weekly: "Shadow Days is about Jen. It really took him a long time to get over her. He really loved her a lot."
They added: "He wrote the song as a farewell letter knowing [Aniston] would hear it. Ultimately he's done a lot of self-reflection though and it he realises they weren't right for each other."
The on-off duo got together in April 2008 and finally called it quits late in 2009.
Jennifer has been with her actor boyfriend Justin Theroux for over a year now.
The source added: "[John and Jen] weren't right for each other, but he is really a good guy.
"He's looking for a nice, non-famous girl he can relate to ... He loved [Jen and Jessica] both but it really affected him emotionally and it wasn't worth it."
Watch the video for Shadow Days:
- Bang! Showbiz