Thilo joined the Nazi party in December 1930 and the SS in 1934. From 1938 to 1941 he worked as a gynaecologist for the Lebensborn organization. After six months of war service he was assigned to the Auschwitz concentration camp in July 1942. There he became responsible for the infirmary camp with the rank of SS-Obersturmführer. Thilo called the camp the "anus mundi" ("anus of the world"). He was one of the physicians commonly performing the "selections" in which incoming Jews were divided into those deemed able to work and those who were gassed immediately.
Thilo also participated in the liquidation of the Theresienstadt family camp on March 8, 1944, when 3,791 Jews were murdered in the gas chambers. In October 1944 Thilo was transferred to Gross-Rosen where he served as camp physician until February 1945. He fled shortly before the camp's liberation. After the war Thilo committed suicide in prison.