The announcement is a massive boost to the club as the Cowboys prepare to host their Telstra Premiership season launch in Townsville on Friday ahead of star half Johnathan Thurston's final season.
The Townsville-born 26-year-old will line up next to Thurston this year before taking over as the chief playmaker in 2019.
Morgan had previously said he did not want to leave the club that signed him as a teenager and he has proved good to his word.
"I'm stoked to be staying at the Cowboys, a club I grew up supporting and, later in life, proudly playing for," Morgan said.