Objective To study the effects of color Doppler ultrasound insonification of maternal rats of different pregnancy periods on the brain ultrastructure of fetal rats. Methods SD rats of different pregnant periods (12 d, 15 d, and 18 d) were insonificated by color Doppler ultrasound for 30 min. The PREIRUS color computer audio-visual device was used with the insonificating parameters as follows: EUP-LTM4,H5.0 MHz,Tis=0.4,and Micd=1.2. The fetal brains of the each group was collected 24 hours after insonification, and the changes of brain ultrastructure were observed by transmission electron microscope (TEM). Results There were no significant changes on brain ultrastructure in fetal rats of 12-day maternal pregnancy, with occasional dissolved mitochondria cristae, slight expansion of endoplasmic reticulum, relatively regular nucleus shape and smaller vacuoles in the cytoplasm. There were obvious changes on brain ultrastructure in fetal rats of 15-day maternal pregnancy, with the injury of organelles being severer than that of 12-day maternal pregnancy. There were significant changes on brain ultrastructure in fetal rats of 18-day maternal pregnancy, with obvious expansion of endoplasmic reticulum, severely irregular nuclear shape, obviously dissolved mitochondrial cristae, expansive nuclear gap and large vacuoles in the cytoplasm. Conclusion Color Doppler ultrasound insonification at different maternal pregnancy periods have different effects on the brain ultrastructure of fetal rats; the earlier the pregnancy period, the smaller the effects on brain ultrastructure of fetal rats.