Cruise ya auri actress Mimi Rogers a ranar 9 ga Mayu, 1987. Sun saki a ranar 4 ga Fabrairun, 1990. Rogers ya gabatar da Cruise ga Ikilisiyar Scientology. Ya sadu da matarsa ta biyu, actress Nicole Kidman, a kan saitin fim din su Days of Thunder (1990). Ma'aurata sun yi aure a ranar 24 ga Disamba, 1990. Cruise da Kidman sun haifi 'ya'ya biyu, Isabella Jane (an haifi 1992) da kuma Connor Antony (an haifi 1995). A watan Fabrairun 2001, Cruise ya nemi saki daga Kidman yayin da ta yi ciki ba tare da saninsa ba. Ciki ya ƙare a cikin zubar da ciki. A shekara ta 2007, Kidman ya bayyana jita-jita game da zubar da ciki a farkon aurenta ga Cruise, yana cewa a cikin wata hira da Cruise, "Ba daidai ba ne", yana bayyana cewa tana da babban ciki na Urban. Kuma kafin ya yi aure, ya yi magana da ni game da ƙaunar da yake da ita ga kowa da kowa, amma har yanzu yana ƙaunata da ni.
Fabrairu shekara ta 2001