He was born as Carl Freiherr Ritter von Heine in Cannstatt near Stuttgart. He came from the famous Heine family.

His grandfather Johann Georg Heine was the first instrument maker for surgery and orthopedic mechanic, and his father and uncles had, according to contemporary descriptions, earned “immortal merits” in the field of orthopedics.

Heine studied in Tübingen and Würzburg. After completing his studies, he traveled and continued his training in Paris, London, Edinburgh, Glasgow, and Dublin.
During the German–Danish War, he gained experience in a Prussian field hospital, which he later published in a work on gunshot injuries of the lower extremities. In 1865, he completed his habilitation in Heidelberg and took over the clinic three years later, after his superior Otto Weber died of diphtheria. One year after that, he accepted the call to Innsbruck as the first holder of the chair.

His place of work was still on the first floor of the hospital building at Marktgraben. It was here that he wrote his famous contributions to the Pitha–Billroth Handbook on hospital gangrene. He became an Austrian citizen and was ennobled by the Emperor.
In 1873, he was commissioned to establish the Second Surgical Clinic in Prague. Among his works were widely read contributions on anus praeter naturalis (artificial anus), prostatic hypertrophy, resection of the larynx for laryngeal stenosis, and the surgical treatment of pseudarthroses (non-unions).

Professor von Heine died in 1877 – at the age of 40 – in Prague, he too a victim of diphtheria. He left to the Prague Medical Faculty an anatomical specimen collection that bears his name.