Lawson Crouse scored two goals for the Canadians, who won all five games at the tournament and outscored the opposition 32-10.
Dylan Strome opened the scoring at 3:34 and Crouse made it a 2-0 game a few minutes later. Mitchell Marner and Travis Konecny added goals later in the first period to silence the crowd at Alcaplast Arena.
"We knew we had to have a really good start against (the Czechs) because they were playing really well," said head coach Jody Hull. "Our guys just bought into the process. It's an amazing group."
The Czechs got on the board early in the second period when Radek Koblizek beat netminder Zach Sawchenko. Nicolas Roy restored Canada's four-goal cushion before Lukas Jasek scored for the Czechs late in the frame.
Crouse added an insurance goal in the third period.
"After our first goal, we just kept rolling," Marner said. "We're a hard team to stop when we play as one and I think we did that very well in this tournament and in the gold medal game."
Canada finished first in Group B in preliminary round play with a 3-0 record and dumped the United States 11-5 in the semifinal on Friday. The Czechs were tops in Group A at 3-0 and defeated Sweden 4-3 to reach the final.
"We tried to keep things simple yet hard enough for other teams to play against us," Hull said. "I'm just proud that every guy bought in to what we were doing as a hockey club."
Sawchenko made 17 saves for the victory. Alex Stezka and Daniel Vladar split goaltending duties for the Czechs, stopping 18 of 24 shots.
The Americans beat Sweden 5-4 to take the bronze medal. Dennis Yan scored the winning goal in the final minute of overtime.
Canada has won the tournament on 19 of 24 occasions since it began in 1991.