We aimed to characterize somatic mutations in the D-loop of mitochondrial DNA (mtDNA) and their impact on survival in oral squamous cell carcinoma patients in an endemic betel quid chewing area. Histologically confirmed oral cancer and corresponding non-tumor tissues were obtained from 59 patients. The D-loop of mtDNA sequence in a patient's non-cancerous tissues was compared with that of paired oral cancer samples and any sequence differences were identified as somatic mutations. With a median follow-up of 16 months, somatic mutations of the D-loop were observed in 38 (64.4%) patients and most of them occurred in the poly-C tract. There was no significant difference between the mutation group and non-mutation group in age, gender, primary site, histological features, pathological stage, smoking, betel quid chewing, alcohol consumption, and postoperative radiotherapy. However, patients with D-loop mutations have better survival (2 year disease specific survival rate: 73.4 vs. 45.0%, P = 0.0374). A high rate of somatic mutations in the D-loop region of mtDNA was found in betel quid-related oral squamous cell carcinoma patients. Somatic mutation of D-loop of mtDNA was associated with better survival.