The Legend of Condor Hero is set in the 13th century at the time of the Mongol invasion of China. Nearly a decade after the end ofThe Legend of the Condor Heroes, the Mongols have now conquered the Jin Dynasty and are now setting their sights towards the Southern Song Dynasty. The citizens of Southern Song, many of them great martial artists of the Central Plains, band together to defend their country from the onset of the Mongol horde. The story culminates in the historic Battle of Xiangyang, which was a critical battle that led to the fall of China to the Mongols.

The story revolves around the young martial arts fighter Yang Guo (Youka), who falls in love with his martial arts master, Xiaolongnü(Shouryuujo), and the trials and tribulations he goes through while searching for his love in war-torn China.

As compared to TVB's prior live action adaptations, the animated version cut out much of the side stories, and changed some of the plots to make the stories to fit into the 30-minute 26 episode blocks, as opposed to the 1-hour 20 episode blocks used in most TVB dramas. As a result, some do not regard it as a canonical adaptation.