He was the second (but eldest surviving) son of Christian I, Duke of Saxe-Merseburg, and Christiana of Schleswig-Holstein-Sonderburg-Glücksburg.
The death of his older brother Johann Georg on 3 January 1654 made him the new heir of the duchy of Saxe-Merseburg.
Christian II's short reign had little impact on the history of the duchy.
In fact, he is only remembered today for one of the obelisks in the gardens of Castle Merseburg, where he appears together with his wife.
In Moritzburg an der Elster on 14 October 1679, Christian married his paternal cousin, Princess Erdmuthe Dorothea of Saxe-Zeitz.