Haywood moved into the starting lineup during his sophomore season, and the Tar Heels earned a #3 seed in the 1999 NCAA tournament, but were eliminated in the first round. The Tar Heels struggled again during the 1999–2000 season, but experienced a resurgence during the 2000 NCAA tournament, reaching the Final Four. The 2000–01 season was Haywood's last at UNC, and the first for new head coach Matt Doherty. That season the Tar Heels earned a #2 seed in the 2001 NCAA tournament, but were eliminated in the second round.
At UNC, Haywood recorded the first triple-double in school history against the University of Miami on December 4, 2000 with 18 points, 14 rebounds and 10 blocks (which was also a UNC record). He also finished his college basketball career as the Atlantic Coast Conference's all-time leader in field goal percentage (63.7%), and is the Tar Heels' all time leader in blocked shots (304). During his senior year, Haywood was named to the All-Atlantic Coast Conference 2nd Team, and also was named 2nd Team All-America by the Sporting News.