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Background It is advisable to clean the palate and tongue thoroughly during oral care to protect against nosocomial infections. However, improper cleaning may cause nausea. To date, no robust data are available regarding how to implement this procedure properly. Furthermore, traditional cotton balls, forceps and normal saline are still used in clinical in China. This mixed methods study aimed to explore the appropriate depth and direction of cleaning methods for palates and tongues without causing nausea and the factors influencing cleaning depth and discomfort in traditional oral care. Methods Our study recruited students (n = 276) from a medical university. The first phase was a quantitative study, in which forceps were slowly inserted into their throats until the gag reflex was triggered, and then, the insertion depth was measured. After that, participants were randomly divided into two groups. In group A, palates and tongues were cleaned coronally and then sagittally, with the converse order used for group B. The extent of nausea was measured. Additionally, the qualitative data were types of discomfort other than nausea reported by the participants. Results The tolerable depths (without causing nausea) for cleaning the palate and tongue were 6.75 ± 1.07 cm and 6.92 ± 1.11 cm, respectively. Participants of male sex and with high BMI (overweight/obese) were associated with greater tolerable cleaning depth. The extent of nausea caused by cleaning both the palate and the tongue sagittally was higher than that elicited by coronal cleaning (p = 0.025 and p = 0.003, respectively). Other discomforts included itching, saltiness and coldness. Conclusion It is appropriate to increase the cleaning depth of the palate and tongue for adult males and overweight/obese individuals. Moreover, coronal cleaning causes lower levels of nausea, and traditional oral care appliances should be improved.