Objective To explore the trend of hypertension prevalence and related factors in Yi people from 1996 to 2015. Methods Three successive cross-sectional surveys were conducted in Liangshan Yi Autonomous Prefecture in 1996, 2007 and 2015, respectively. A total of 8448 participants aged 20-80 years (5040 Yi farmers, 3408 Yi migrants) were included in final analysis. Results Overall, the age-standardised prevalence of hypertension in migrants was significantly higher than in farmers. Furthermore, the age-standardised prevalence rates increased from 10.1% to 15.3% to 19.6% in Yi migrants and from 4.0% to 6.3% to 13.1% in Yi farmers during 1996 to 2007 to 2015. The highest 2015-to-1996 ratio of age-standardised hypertension prevalence was in male farmers (ratio=4.30), whereas despite the highest prevalence of hypertension, the equivalent figure in male migrants was 1.57. The older age, overweight and obesity were persistent risk factors of hypertension in three periods. After adjusted for age and body mass index, the difference of hypertension prevalence between 1996 and 2015 then vanished in male migrants (OR=1.335; 95% CI: 0.884 to 2.015) and female farmers (OR=1.267; 95% CI: 0.590 to 2.719). The disparities of hypertension prevalence between Yi migrants and farmers were not statistically significant in all subgroups when adjusted for age, body mass index and education. Conclusions Over the past two decades, the hypertension prevalence in Yi people has significantly increased. Yi migrants were more likely to be hypertensive than Yi farmers which was predominantly driven by the discrepancy of body mass index between them.