Abstract: Objective To investigate the effect of irisin gene polymorphism on target organ dysfunction in young and middle-aged hypertensive patients. Methods From June, 2016 to August, 2017, 100 young and middle-aged hypertensive patients in our hospital were selected as an observation group, and 100 healthy adults were served as a control group. The polymorphic distributions of irisin genes between the two groups were compared. At the same time, the relationship between target organ dysfunction and irisin gene polymorphism in young and middle-aged hypertensive patients were analyzed. Results When compared with the control group, the observation group patients got decreased serum irisin expression[(2.52±0.75) μg/ml vs. (2.97±0.80) μg/ml, P<0.001]. The cases of rs16835198 genotype TT, GT and GG in the observation group were 20, 38 and 42, respectively, while they were 29, 48 and 23 in the control group with a statistically significant difference (P=0.015). When compared with the patients with irisin ≥ 3 μg/ml, patients with Irisin<3 μg/ml got increased thickness of carotid artery intima[(1.27±0.17) mm vs. (1.19±0.16) mm, P=0.019)] and decreased level of ejection fraction[(59.88±4.87)% vs. (63.28±5.29)%, P=0.001]. The carotid artery intima in young and middle-aged hypertensive patients with GG, GT and TT of rs16835198 were (1.32±0.18) mm, (1.16±0.17) mm and (1.21±0.18) mm, and there was a statistically significant difference (P<0.05). Conclusion The irisin gene is polymorphic distribution in young and middle-aged hypertensive patients, which is related to the impairment of target organ function in patients.