This study aimed to apply longitudinal data (in four waves) to examine relationships between body mass index (BMI), flexibility, muscular endurance, and explosive power, and employed a random-intercept panel model (RIPM) to divide the variations of different waves into between- and within-person variations. Furthermore, a multi-group model test was conducted to explore whether an interaction effect existed between sex and these relationships. The data were collected from a university in Taiwan between August 2009 and July 2010, and 3863 freshman and junior students were recruited. Results showed that the between- and within-person relationships between BMI and explosive power, and between BMI and muscular endurance, were negative (independent of sex). The negative between- and within-person associations between BMI and muscular endurance were both invariant with respect to sex. The negative between-person associations between BMI and explosive power were not equivalent for both sexes, yet the within-person associations between BMI and explosive power were equivalent for both sexes. The between-person associations between BMI and flexibility were positive for both sexes, but the within-person associations of these two variables were negative for both sexes. The invariance test confirmed that the positive associations of between-person BMI and between-person flexibility were invariant for both sexes, yet the negative associations of within-person BMI and within-person flexibility were not equivalent for both sexes. Between-and within-person correlations among explosive power, muscular endurance, and flexibility were significantly positive. Only the auto-regressions of BMI and muscular endurance were significant and equivalent for both sexes.