The team logo is a stylized version of the flag of Ohio, which is a burgee (i.e. swallowtail pennant), in the form of a "C" wrapped around a star, representing both patriotism and Columbus' status as state capital. Previously used as an alternate logo starting in 2003, it became the primary logo as part of a Reebok-sponsored redesign for the 2007–08 season. The original logo had a red ribbon with 13 stars representing the 13 Colonies, unfurled in the shape of the team's initials, CBJ, with an electric gold hockey stick cutting through the center to represent the "J." An additional star atop the stick represented Columbus' status as state capital. From 2003 to 2015, the team's jerseys featured an alternate logo, a Civil War cap with crossed hockey sticks, on the shoulders.

The Blue Jackets unveiled a new third jersey in the 2010–11 season, using a vintage hockey jersey design. In the spirit of its Civil War theme, it sports a union blue base with white stripes on the sleeves and on the shoulder padding. The crest features the team's Civil War-era cannon. It honors the team's founder, John H. McConnell, with his initials on the neckline, as well as its slogan "We fight, we march!" on the inside of the collar. During the 2015 NHL Draft, it was revealed that the cannon crest had replaced the hat logo on the shoulders of the home and away jerseys, with a color change to match the jerseys' color scheme.