Abstract: Objective To observe and analyze the different functional areas of cerebral cortex in C57BL/6 mice of different months. Methods Improved alkaline phosphatase staining was used to reveal the microvascular morphology of the cerebral cortex of C57BL/6 mice, including motor cortex (primary motor cortex, secondary motor cortex), sensory cortex (primary somatosensory cortex, secondary somatosensory cortex), visual cortex (primary visual cortex, secondary visual cortex), auditory cortex (primary auditory cortex, secondary auditory cortex), olfactory cortex (extrorhinal cortex, entorhinal cortex). Images were captured by OLMPUS BX51 microscope combined with Image-Pro Plus 5.1 software. The microvascular length density (Lv), microvascular surface area density (Sv) and microvascular volume density (Vv) were analyzed by Image-Pro Plus 5.1 software. Results The levels of alkaline phosphatase in microvessels of different functional areas of cerebral cortex increased with age and reached the peak in adults. There were four patterns for pia vessels to enter the cortex including T shape, Y shape, large arc, small arc. The Lv, Sv and Vv in different functional areas of the same aged mice showed a downtrend trend in the motor cortex, sensory cortex, visual cortex, auditory cortex and olfactory cortex. Moreover, the microvascular density of Lv, Sv and Vv in the motor cortex and sensory cortex was statistically significant compared with those in the olfactory cortex (P<0.05). The vascular densities of different functional areas in the aged mice were lower than those in the adult ones, but there was no statistical significance (P>0.05). Conclusion The improved alkaline phosphatase staining may clearly reveal the microvascular architecture in cerebral cortex of C57BL/6 mice and it provides morphological reference for the research of cerebrovascular diseases and the preparation of animal models.