Objective To investigate the application of different sequence scan of MRI in the diagnosis of neonatal hypoxic ischemic encephalopathy (HIE). Methods The MRI images of 32 children with clinically diagnosed HIE were retrospectively analyzed. Conventional magnetic resonance imaging (MRI), diffusion weighted imaging (DWI) and its apparent diffusion coefficient (ADC) and magnetic susceptibility weighted imaging (SWI) can were used to evaluate the application of different scanning sequences in the diagnosis of HIE. Results The positive rate of conventional MRI+SWI+DWI in the diagnosis of HIE (90.63%) was significantly higher than that of conventional MRI+SWI (65.63%), conventional MRI+DWI (59.38%) and conventional MRI (43.75%) (P＜0.05). 12 cases of HIE were detected by conventional MRI, including 5 cases showing T1 high signal. 8 cases showing T2 high signal and cinereum matter was without clear boundaries. 19 cases with HIE were detected by MRI+DWI, including 10 cases of basal ganglia, thalamus and other areas showing high signal on DWI images, patchy in distribution and signal decline on ADC images. 21 cases of HIE were detected by conventional MRI+DWI+SWI, including 16 cases showing low signal, the SWI images showed a fanshaped, spot-like and patchy in distribution on SWI images. Conclusion The combined MRI+SWI+DWI sequence can improve the diagnostic accuracy of HIE.