Objective This study aimed to investigate the expression of HOX transcript antisense intergenic RNA (HOTAIR) in salivary adenoid cystic carcinoma (SACC) and explore its influence on prognosis. Methods A total of 86 cases of patients with SACC who underwent surgical resection treatment from March 2007 to March 2014 were selected. In the same period, 45 cases of normal salivary gland tissues were obtained. The expression of HOTAIR was detected via real-time fluorescent quantitative polymerase chain reaction. The patients were followed up after the surgery, and the follow-up deadline was March 31, 2019. The deaths and survival times of patients were recorded. Based on the quartile value of the relative expression level of HOTAIR in SACC patients, the patients were divided into low expression group and high expression group. Kaplan-Meier method and Log-Rank test were used to compare the survival time of the two groups. Taking the age, sex, tumor location, pathological type, tumor diameter, TNM stage, nerve invasion and lymph node metastasis as independent variables, Cox proportional hazards regression model was used to analyze the multiple factors affecting survival time. Results The relative expression of HOTAIR in SACC tissue was 2.48±0.22, which was higher than that in normal salivary gland tissue at 1.03±0.13, and the difference was statistically significant (t=39.812, P<0.001). No nerve invasion and lymph node metastasis were observed in these patients compared with those patients with TNM stages Ⅰ or Ⅱ, while the relative expression of HOTAIR in the tissues of patients with TNM stages Ⅲ or Ⅳ, nerve invasion, and lymph node metastasis increased (P<0.05). Kaplan-Meier survival analysis showed that the average survival time and cumulative survival rate in the low expression group were higher than those in the high expression group [(113.32±10.77) months vs. (59.75±6.50) months and 72.73% vs. 39.06%, respectively, P=0.004]. Cox proportional hazard regression analysis showed that nerve invasion, lymph node metastasis, and the high expression of HOTAIR were the independent risk factors for the prognosis of patients with SACC (HR=3.274, 2.971, and 2.911, respectively, P<0.05). Conclusion HOTAIR was highly expressed in patients with SACC tissues and associated with poor prognosis. It is a risk factor for prognosis, and it is expected to be a potential marker for the prognostic assessment of patients with SACC.