NOP2/Sun RNA methyltransferase 2 (NSUN2), encoded by the NSUN2 gene, is a nuclear RNA methyltransferase that catalyzes the methylation of cytosine to 5-methylcytosine (m5C). Although RNA modification has been widely discussed in cancer development and prognosis, the role of the NSUN2 gene in oral cavity squamous cell carcinoma (OCSCC) is unclear. This was a retrospective, case-control study. A total of 2514 participants were enrolled, including 52.4% (1318/2514) diagnosed with OCSCC and others as health control. The impact of NSUN2 rs4702373, rs166049, rs13181449, and rs8192120 on cancer development and prognosis were analyzed. Our results revealed that NSUN2 rs13181449 allele TT was significantly associated with lower OCSCC risk, with an adjusted odd ratio (AOR) [95% confidence index (CI)] of 0.757[0.575-0.997]. For cigarette smokers, the impact of rs13181449 was more obvious that AOR [95% CI] of allele CT, TT, and CT+TT were 0.760 [0.583-0.991], 0.699 [0.493-0.990], 0.746 [0.580-0.960], respectively. For OCSCC patients, rs4702373 allele CT was independently associated with advanced histological grade. Expression levels between different allele mutations were various in the GTE database. Mutant rs4702373 and rs166049 were associated with higher expression than the wild type, conversely mutant rs13181449 had lower expression. In the TCGA database, the trend that patients with higher expression had worse survival than those with lower expression was shown. In conclusion, NSUN2 rs13181449 was associated with lower cancer risk, especially for cigarette smokers. Unlikely other allele mutations, rs13181449 was correlated to lower expression. Patients with higher expression had worsened clinical outcomes.