Poor oral hygiene is an established risk factor of head and neck cancer (HNC); however, its role in the survival of HNC is unclear. We investigated the association between oral hygiene habits, including regular dental visits, frequency of tooth brushing, and use of dental floss, and the overall survival (OS) of HNC using interview data collected from 740 HNC patients. We found that poor oral hygiene was significantly associated with a worse OS of HNC (hazard ratio (HR) = 1.38, 95% confidence interval (CI): 1.03-1.86). Furthermore, this relationship was modified by the single nucleotide polymorphism, rs11536889, of TLR4. A strong association between poor oral hygiene and a worse survival of HNC was observed among those with the CG or CC genotype (HR = 2.32, 95% CI: 1.41-3.82) but not among those with the GG genotype (HR = 0.95, 95% CI: 0.65-1.40). Overall, our results indicated that poor oral hygiene, a risk factor of HNC, may also be a prognostic factor of HNC. More investigations are needed to determine the biological mechanisms to explain the worse HNC survival associated with poor oral hygiene.