This study aims to reveal the structure of the Yi Sunsin turtle ship by considering the ways how a total of 19 naval guns were arranged in the turtle ship. According to the results of this study, two largest guns (cheonja chongtong) were placed at the front of the ship on the second floor; two second-largest guns (jija chongtong) at the front on the third floor; one third-largest gun (hyeonja chongtong) at the front on the third floor; two third-largest guns at the rear end on the third floor; twelve fourth-largest guns (hwangja chongtong) along the side on the third floor. The findings on the deployment of naval guns support the hypothesis that the Yi Sunsin turtle ship had a three-story structure.