He was the second (but eldest surviving) son of Christian I, Prince of Anhalt-Bernburg by his wife Anna of Bentheim-Tecklenburg, daughter of Arnold III, Count of Bentheim-Steinfurt-Tecklenburg-Limburg.

During the years 1608-1609 he studied in Geneva with his cousin John Casimir of Anhalt-Dessau accompanied by two tutors, Markus Friedrick Howell and Peter von Sebottendorf.

In 1618, at the age of nineteen, Christian recorded the horror of the beginning of the Thirty Years' War; in his diary, he wrote that his duty to fight was "ma fatale destinée."

During the first year of his reign, Bernburg was plundered by troops under the Danish General Heinrich Holk and an epidemic fever killed almost 1,700 inhabitants.

In 1636 Schloss Bernburg was almost taken by the marauding troops, but the great courage of the seventy-year-old Hofmarschall Burkhard von Erlach prevented this.