Objective To study the application value of bedside ultrasound in the diagnosis of neonatal craniocerebral diseases. Methods A total of 94 high risk neonates accepted bedside color doppler ultrasound examination in our hospital from February 2015 to July 2016 were taken as the clinical research objects. The color doppler ultrasound and MRI result of the craniocerebral were compared and analyzed. Results There were no significant differences in clinical detection rates of intracranial hemorrhage level II, III and IV, hypoxic ischemic encephalopathy, ventriculomegaly, intracerebral hemorrhage and purulent meningitis between color doppler ultrasound and MRI(P＞0.05), the clinical detection rate of beside doppler ultrasound in the diagnosis of choroid plexus cyst, subependymal cysts and intracranial hemorrhage level I was significantly higher than that of MRI(P＜0.05), the clinical detection rate of MRI in the diagnosis of subarachnoid hemorrhage and subdural hemorrhage was significantly higher than that of beside doppler ultrasound(P＜0.05). Partial diagnosis results were confirmed by operation or autopsy. Conclusion Compared with MRI, bedside doppler ultrasound has high detection accuracy of choroid plexus cyst, intracranial hemorrhage level I and subependymal cysts in neonates, and which deserve generalization.