Dubois' contract is worth $3.35 million in the first year and $6.65 million in the second.
The 22-year-old scored 18 goals in 2019-20 and led the Blue Jackets in both points and assists with 31 and 49, respectively. He has tallied 65 goals and 93 assists in 234 career games with Columbus.
"Pierre-Luc is a talented, young player with great potential, and we look forward to his continued growth and development, and the valuable contributions he will bring to our team," said Blue Jackets GM Jarmo Kekalainen in a release.
Dubois has not missed a game during his first three seasons, and has recorded two 20-goal and 30-assist campaigns during his young NHL career. He is the fastest Blue Jackets player to record 100 career points, needing just 143 games to hit the milestone.
"I'm excited to have the contract done and to be able to get back on the ice and play hockey again, especially with everything that is going on in the world right now," said Dubois. "I'm very fortunate and looking forward to being with my teammates at camp and the start of a new season."