Previous studies have reported that a high free fat mass (FFM) was associated with elevated blood pressure in children. However, the observed relationship could be confounded by body weight. Thus, we performed cross-sectional analyses to understand the differences between the percentage of free fat mass (FFM%) and FFM in relation to blood pressure in healthy Chinese children. A total number of 2671 (1264 girls; aged 6-14 years) healthy Chinese children was recruited in 2014 (baseline). We further prospectively examined whether these indices predicted hypertension risk during the 2 years of follow-up (2014-2016) among 2094 participants who were free of hypertension at the baseline. Blood pressure was repeatedly measured in 2014, 2015 and 2016. Hypertension was defined as either high systolic blood pressure and/or high diastolic blood pressure (≥age- and sex-specific 95 percentile for Chinese children). The baseline FFM was assessed by bio-impedance analysis, and FFM% was calculated as FFM divided by the body weight. A high FFM was associated with a high baseline blood pressure and high hypertension risk after adjustment for potential confounders (all p < 0.001). By contrast, a high FFM% was associated with a low baseline blood pressure and low hypertension risk in the fully adjusted model (all p < 0.001). Each one-percent increment of FFM% was associated with a 9% lower risk of developing hypertension (adjusted hazard ratio = 0.91; 95% confidence interval: 0.89, 0.94). A high FFM% was associated with a low blood pressure and low hypertension risk in healthy Chinese children.