Objective To explore the differences in the prevalence of hypertension (HTN) between Tajik and Kyrgyz residents in Tashkurgan Tajik Autonomous County, Xinjiang, analyze the associated factors for HTN in the two ethnic groups in this area, and provide a scientific basis for formulating targeted HTN prevention and control strategies in border ethnic areas. Methods A total of 19785 Tajik and 605 Kyrgyz permanent residents who completed the annual physical examination in Tashkurgan County in 2024 were included as study participants. Baseline data, including demographic characteristics, lifestyle, past medical history and physical examination findings were collected. The differences in the prevalence of HTN and baseline data between the two ethnic groups were compared, and the independent risk factors for HTN were analyzed using a multivariable logistic regression model. Results The prevalence of HTN in the Tajik ethnic group was 22.4%, which was significantly higher than 17.4% in the Kyrgyz ethnic group (P=0.003). There were statistically significant differences between the two ethnic groups in age structure, occupational distribution, family history of HTN, smoking status, physical exercise participation rate and body mass index (BMI) classification (P<0.05). Multivariable logistic regression analysis showed that increased age (45-59 years and ≥60 years), engaging in agriculture, forestry, animal husbandry and fishery, having a family history of HTN, overweight and obesity by BMI, non-smoking, and Tajik ethnicity were independent risk factors for HTN in residents of this area (P<0.05). The negative correlation between smoking and HTN was caused by population selection bias under the special plateau environment, and it did not mean that smoking had a protective effect. Conclusion The risk of HTN in the Tajik ethnic group in Tashkurgan County is significantly higher than that in the Kyrgyz ethnic group. The occurrence of HTN is the result of the combined action of genetic factors and environmental factors such as the plateau environment, lifestyle and occupational characteristics. Targeting high-risk groups such as older adults and farmers and herdsmen, intervening in weight and improving lifestyle in combination with ethnic characteristics, and continuously promoting tobacco-control education are the key measures to reduce the risk of HTN in ethnic populations in this area.