Münch was the brother of conductor Eugen Münch and uncle of conductor and composer Hans Münch. His son Charles Munch was a famous symphonic conductor and violinist who had a long association with the Boston Symphony Orchestra. His daughter Emma married Paul Schweitzer, Albert Schweitzer's brother. His son Fritz Münch succeeded him as conductor of the Wilhelmer Choir and was director of the Strasbourg Conservatory for several years.
Sources
Albert Schweitzer: Memories of Ernst Münch (1945). In: Essays on Music, ed. Stefan Hanheide, Bärenreiter-Verlag, Kassel and Basel, 1988, ISBN3-7618-0920-4, p. 185-194.