The computed tomography angiography (CTA) postprocessing manually recognized by technologists is extremely labor intensive and error prone. We propose an artificial intelligence reconstruction system supported by an optimized physiological anatomical-based 3D convolutional neural network that can automatically achieve CTA reconstruction in healthcare services. This system is trained and tested with 18,766 head and neck CTA scans from 5 tertiary hospitals in China collected between June 2017 and November 2018. The overall reconstruction accuracy of the independent testing dataset is 0.931. It is clinically applicable due to its consistency with manually processed images, which achieves a qualification rate of 92.1%. This system reduces the time consumed from 14.22 ± 3.64 min to 4.94 ± 0.36 min, the number of clicks from 115.87 ± 25.9 to 4 and the labor force from 3 to 1 technologist after five months application. Thus, the system facilitates clinical workflows and provides an opportunity for clinical technologists to improve humanistic patient care.