In December 1917, he married L. Mae, with whom he had one son and two daughters: Clark Shaughnessy, Jr.; Janice Shaughnessy, and Marcia Wilson. He met his wife in New Orleans while coaching at Tulane. A teetotaler, Shaughnessy held a negative opinion of both drinkers and smokers. Marchmont Schwartz noted, "When he said, 'Let's go have a drink,' he meant, 'Let's go drink a milk shake ... He disappointed a lot of newspapermen that way." Aside from his declared hobby as a football coach and experimenter, he enjoyed long-distance driving. Shaughnessy preferred to devise plays late at night, between midnight and dawn, while his household slept. A 1977 "Sports Illustrated" article described him as an "ascetic" and his lifestyle as "Spartan". It noted he would go to bed as early as 7 o'clock, and wake up for work at three or four in the morning.