Purpose: To examine the effects of three types of school-based exercises on bone health and physical fitness function in Chinese boys and girls. Methods: One hundred and seventy-four Chinese boys and girls were randomly assigned into four groups: (1) sham exercise (ShEx); (2) high-impact exercise (HiEx); (3) high-impact exercise with various directions (HiExVi); and (4) high-intensity interval exercise (HiInEx). Speed of sound (SOS) and physical fitness parameters were determined before and after six-month intervention. Results: At the end of six-month intervention, participants in all groups show an increment of SOS compared with the baseline (p < 0.05), and the changes were higher in HiEx (mean: 38.878 m/s, 95% CI: 32.885~44.872, p = 0.001) and HiExVi groups (49.317 m/s, 42.737~55.897, p < 0.001) compared with ShEx group (20.049 m/s, 13.751~26.346). Six-month exercise training generated a reduction of percent of body fat (PBF) and waist–hip ratio (WHR) (p < 0.05). The decrease of PBF was greater in HiExVi (−1.222%, −1.820~−0.624, p = 0.012) and HiInEx groups (−1.395%, −1.809~−0.982, p = 0.003), whereas the reduction of WHR was larger in HiEx (−0.026, −0.039~−0.014, p = 0.009), HiExVi (−0.024, −0.036~−0.012, p = 0.021), and HiInEx groups (−0.035, −0.046~−0.024, p < 0.001) compared with ShEx group. Balance function (BLF), vital capacity (VC), standing long jump (SLJ), and sit up (SU) increased in all intervention groups (p < 0.05). The BLF increased in HiEx (6.332 s, 4.136~8.528, p = 0.001), HiExVi (10.489 s, 8.934~12.045, p < 0.001), and HiInEx groups (9.103 s, 7.430~10.776, p < 0.001) showed a greater change than that of ShEx group (1.727 s, 0.684 ~2.770). The increment of VC (273.049 mL, 199.510~346.587, p < 0.001) and SU (2.537 times/min, 0.639~4.435, p = 0.017) was higher in HiInEx group, whereas the accrual in SLJ was larger in HiExVi (7.488 cm, 4.936~10.040, p = 0.007) compared with ShEx group (58.902 mL, 7.990 ~109.814; −0.463 times/min, −2.003~1.077; 1.488 cm, −0.654 ~3.630). Conclusion: The brief school-based exercises were effective in improving schoolchildren’s health, but they showed different effects, with HiEx mostly improving bone health, HiInEx largely benefiting physical fitness function, and HiExVi enhancing both bone and physical fitness.