This study was to explore the application of deep learning neural network (DLNN) algorithms to identify and optimize the ultrasound image so as to analyze the effect and value in diagnosis of fetal central nervous system malformation (CNSM). 63 pregnant women who were gated in the hospital were suspected of being fetal CNSM and were selected as the research objects. The ultrasound images were reserved in duplicate, and one group was defined as the control group without any processing, and images in the experimental group were processed with the convolutional neural network (CNN) algorithm to identify and optimize. The ultrasound examination results and the pathological test results before, during, and after the pregnancy were observed and compared. The results showed that the test results in the experimental group were closer to the postpartum ultrasound and the results of the pathological result, but the results in both groups showed no statistical difference in contrast to the postpartum results in terms of similarity ( P > 0.05 ). In the same pregnancy stage, the ultrasound examination results of the experimental group were higher than those in the control group, and the contrast was statistically significant ( P < 0.05 ); in the different pregnancy stages, the ultrasound examination results in the second trimester were more close to the postpartum examination results, showing statistically obvious difference ( P < 0.05 ). In conclusion, ultrasonic image based on deep learning was higher in CNSM inspection; and ultrasonic technology had to be improved for the examination in different pregnancy stages, and the accuracy of the examination results is improved. However, the amount of data in this study was too small, so the representative was not high enough, which would be improved.