Arterial spin labeling (ASL) is a powerful MRI technique used to noninvasively measure cerebral blood flow (CBF). In preclinical studies, rodent brain CBF serves as an important indicator in many brain disease models. In this work, we established a whole-brain CBF atlas based on 102 adult normal mice and profiled CBF distributions in 27 brain regions. We found that there is a high correlation of CBF between the left and right hemispheres. Additionally, the high-resolution mouse CBF atlas can be used to distinguish mice with autism disorder, indicating the potential applications of the atlas in preclinical studies.