Hypertension is a major risk factor for stroke, atherosclerosis, and other cardiovascular diseases, and obesity is a major risk factor for hypertension. The aim of this longitudinal study was to investigate sex differences in the correlations among obesity-related indices and incident hypertension in a large Taiwanese cohort. We included 21,466 enrollees in the Taiwan Biobank and followed them for 4 years. Of the 21,466 patients enrolled in this study, 6899 (mean age, 49.6 ± 10.9 years) were male and 14,567 (mean age, 49.7 ± 10.0 years) were female. Data on visceral adiposity index (VAI), waist-to-height ratio (WHtR), waist-to-hip ratio (WHR), lipid accumulation product (LAP), conicity index (CI), body roundness index (BRI), body mass index (BMI), body adiposity index (BAI), and abdominal volume index (AVI) were collected and analyzed. The results showed that all of the studied obesity-related indices were significantly associated with incident hypertension. Among them, WHtR was the strongest predictor of hypertension in both sexes. In addition, interactions between VAI, LAP, CI, BMI, and AVI with sex on incident hypertension were also statistically significant. CI and AVI were more strongly associated with hypertension in the men than in the women, while VAI, LAP, and BMI were more strongly associated with hypertension in the women. In conclusion, the studied obesity-related indices were found to be predictors of incident hypertension, and there were differences in the associations between the male and female participants. Our findings may imply that reducing body weight may be associated with a lower risk of developing hypertension.