Morgenstern began his ski jumping career in the Continental Cup, winning three events out of four attempts.

[3] At the start of the 2003–04 season, Morgenstern suffered a violent accident in Kuusamo, in which he was hit by a gust of wind just after takeoff, forcing him to flip over in mid-air and land hard on his back.

[6] During the 2006 Winter Olympics, he won the gold medals in the individual and team large hill competitions.

Further, by reaching the 3rd place in the normal hill event he won his first individual medal at world championships.

During the 2008–09 season, Morgenstern could not win any competition, but won a team gold medal at the Nordic World Ski Championships in Liberec.

However, Morgenstern won gold medals in the team events at the Ski-Flying World Championships and the 2010 Winter Olympics.

On 10 January 2014, he suffered serious head injuries during training for the ski flying event in Bad Mitterndorf.