Our study aimed to investigate the measurement of frontal lobe volume and thalamic volume in fetuses with congenital heart disease (CHD) at different gestational weeks using three dimensional (3-D) ultrasonography and its clinical value. Then, 238 pregnant women who received obstetric ultrasonography in ultrasound department of Internal Medicine of our hospital were enrolled between March 2013 to April 2014. In this study, 85 fetuses were diagnosed to develop CHD by prenatal fetal echocardiography, and the other 153 fetuses were normal. Frontal lobe volume, thalamic volume and cerebral blood flow was determined by color Doppler ultrasonic diagnostic apparatus (type: GE Voluson E8). The level of MCA-PI and CPR in CHD fetus group performed significantly lower than that in normal fetus group (P<0.05), but the level of UA-PI performed significantly higher than that in normal fetus group (P<0.05). When gestational age <30 weeks, there was no significant difference in thalamic volume and frontal lobe volume between the two groups (P<0.05); when gestational age <30 weeks, the level of CHD fetus group performed significantly lower thalamic volume and frontal lobe volume than that in normal fetus group (P<0.05). When gestational age <30 weeks, there was no significant difference in BPD, HC, and GA between the two groups (P<0.05); when gestational age <30 weeks, the level of BPD, HC and GA in CHD fetus group performed significantly lower than that in normal fetus group (P<0.05). If gestational age <30 weeks, CHD performed a small impact on fetal frontal lobe volume and thalamic volume; if gestational age <30 weeks, the level of frontal lobe volume and thalamic volume in fetuses with CHD performed significantly lower than that in normal fetuses.