The six-year-old was diagnosed with first stage cancer at the tender age of four in early 2014.
The cine-icon replied to a tweet, where he mentioned that Ayaan's "strength is unbeatable".
"Thank you for being such a brave father... And to Ayaan, what can one say... his strength and will is unbeatable," Big B tweeted.
The message for the father-son duo came after Emraan called the 'Piku' star an "original super hero".
"Thanks Amitabh Bachchan for the note. Ayaan aspires to be Batman. And Batman aspires to be you. You are the original superhero," Emraan had written.
The 'Azhar' actor has penned a book about his struggles with his son Ayaan's cancer treatment.