During the 2008–09 season, Krejčí scored his first NHL hat-trick on 18 December 2008 against the Toronto Maple Leafs. He registered his first two goals against starter Vesa Toskala and his third against Curtis Joseph in an 8–5 Bruins win. About the midpoint of that season, NESN's play-by-play TV announcer Jack Edwards for televised Bruins games gave Krejčí the nickname "The Matrix", due to his ability to slow down the pace of a game through his skating style and abilities on the ice. Before a game on 2 April 2009, Krejčí was named the winner of the Boston Bruins' 2009 Seventh Player Award. The award is given annually to the player who "goes beyond the call of duty and exceeds all expectations" throughout the course of the season. During the game, Krejčí assisted on a goal by Milan Lucic, the 2008 winner of the Seventh Player Award, in a 2–1 home ice victory over the Ottawa Senators. He completed his second NHL season with a then-career-high 73 points in 82 games to go with a league-high +37 plus-minus rating. On 2 June 2009, he signed a multi-year contract extension with the Bruins, reportedly a three-year contract paying an average of $3.75 million per year.
After the Bruins' 2007–08 season ended, Krejčí was named to the Czech national team on 26 April 2008, for the 2008 IIHF World Championships. He was named to the Czech national team for the 2010 Winter Olympics, playing centre on a line with wingers Tomáš Fleischmann and Martin Erat to open the Games.