Although small toothed whales are sometimes exposed to novel captive environments, the factors that affect their habituation are still unknown. Sex, age, and other individuals are thought to influence their response to novel stimuli. We observed the habituation process of six species, including short-finned pilot whales (Globicephala macrorhynchus), melon-headed whales (Peponocephala electra), Risso’s dolphins (Grampus griseus), common bottlenose dolphins (Tursiops truncatus), rough-toothed dolphins (Steno bredanensis), and striped dolphins (Stenella coeruleoalba) to a novel captive space for 30 days and analyzed the factors affecting their habituation. The evaluated factors were observational days, sex, body length, number of individuals living together, number of feedings per day, and total forced feeding and hydration during the entire observational period. The results showed that all the species become habituated as the days passed. Additionally, the analysis by a cumulative linear model confirmed that the speed of habituation was sex-dependent in some species. The habituation in some species was positively related to the factors excluding observational days and sex, and habituation in the others was negatively related.