Malignant transformation of oral potentially malignant disorders (OPMDs) is a potential cause of oral cancer. Currently, there is no research investigating the rate of malignant transformation of OPMDs into oral cancer in indigenous Taiwanese peoples. This study aimed to retrospectively investigate whether ethnicity (indigenous vs non-indigenous people) plays a role in increasing the malignant transformation rate of OPMDs into oral cancer. This study used data from the oral mucosal screening database and the Cancer Registry File, both of which originated from the National Health Insurance Research Database. We matched the baseline characteristics to control for confounding factors between indigenous peoples and non-indigenous peoples (17,768 indigenous subjects vs 71,072 non-indigenous subjects; 1:4 match) and compared the 2 cohorts. After matching for confounding factors such as age, sex, habits, and OPMD subtype, the malignant transformation rate was not statistically higher for indigenous people than for non-indigenous people. We also discovered that indigenous people with oral verrucous hyperplasia might have a higher chance of malignant transformation into oral cancer than the non-indigenous cohort. We conclude that ethnicity is not a risk factor for the malignant transformation of OPMDs into oral cancer; however, indigenous people with oral verrucous hyperplasia need to pay special attention and are suggested to undergo regular follow-ups for the occurrence of oral cancer.