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Staple food preference vary in populations, but evidence of its associations with obesity phenotypes are limited. Using baseline data (<i>n</i> = 105,840) of the Regional Ethnic Cohort Study in Northwest China, staple food preference was defined according to the intake frequency of rice and wheat. Overall and specifically abdominal fat accumulation were determined by excessive body fat percentage and waist circumference. Logistic regression and equal frequency substitution methods were used to evaluate the associations. We observed rice preference (consuming rice more frequently than wheat; 7.84% for men and 8.28% for women) was associated with a lower risk of excessive body fat (OR, 0.743; 95%CI, 0.669–0.826) and central obesity (OR, 0.886; 95%CI, 0.807–0.971) in men; and with lower risk of central obesity (OR, 0.898; 95%CI, 0.836–0.964) in women, compared with their wheat preference counterparties. Furthermore, similar but stronger inverse associations were observed in participants with normal body mass index. Wheat-to-rice (5 times/week) reallocations were associated with a 36.5% lower risk of normal-weight obesity in men and a 20.5% lower risk of normal-weight central obesity in women. Our data suggest that, compared with wheat, rice preference could be associated with lower odds ratios of certain obesity phenotypes in the Northwest Chinese population.