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The desirable distribution of three major nutrients intake to prevent hypertension is not established. This study is to clarify the relationship between the prevalence of hypertension and the rate of intake of three major nutrients. This is a large-scale cross-sectional study. We analyzed Japanese subjects who had their annual medical examination at St Luke's International Hospital, Tokyo from January 2004 to June 2010. The amount of three major nutrients and salt intake were checked by a questionnaire method, and this study clarified the relationship between the prevalence of hypertension and the rate of three major nutrients with adjustment for age, sex, body mass index (BMI), smoking, dyslipidemia, diabetes mellitus, hyperuricemia, and salt intake. We analyzed 89,851 subjects. Of those, the number of hypertensive subjects was 13,926 (15.5%). The hypertensive group had significantly higher rate of calories from protein (19.7% vs. 19.4%, P < 0.001) but lower rate of calories from fat (16.1% vs. 16.4%, P < 0.001) than that in the non-hypertensive group. The rate of calories from carbohydrate was almost the same between the two groups (64.2% vs. 64.2%). After multiple adjustments, high rate of calories from protein was associated with high prevalence of hypertension (odds ratio: 1.011, 95% confidence interval (CI), 1.005-1.017), as well as aging, male, high BMI, smoking habits, dyslipidemia, diabetes mellitus, and hyperuricemia. High rate of calories from protein could be associated with high risk of hypertension. Therefore, protein-restricted diet may have a favorable effect in preventing hypertension and cardiovascular diseases.