The effect of selenium on hypertension is inconclusive. We aimed to study the relationship between selenium intake and incident hypertension. Adults (age ≥20 years) in the China Health and Nutrition Survey were followed up from 1991 to 2011 (N = 13,668). The latent class modeling method was used to identify trajectory groups of selenium intake. A total of 4039 respondents developed hypertension. The incidence of hypertension was 30.1, 30.5, 30.6, and 31.2 per 1000 person-years among participants with cumulative average selenium intake of 21.0 ± 5.1, 33.2 ± 2.8, 43.8 ± 3.6, and 68.3 ± 25.2 µg/day, respectively. Region and selenium intake interaction in relation to hypertension was significant. In the multivariable model, cumulative intake of selenium was only inversely associated with the incident hypertension in northern participants (low selenium zone), and not in southern participants. Compared to selenium intake trajectory Group 1 (stable low intake), all three trajectory groups had a low hazard ratio for hypertension among the northern participants. However, Group 4 (high intake and decreased) showed an increasing trend of hypertension risk in the south. In conclusion, the association between selenium intake and the incidence of hypertension varied according to regions in China. In the low soil selenium zone, high selenium intake might be beneficial for hypertension prevention.