Objective: Collateral circulation represents an endogenous anastomotic route that serves to compensate for the stenosis or occlusion of intracranial arteries. It supplies collateral blood flow, thereby sustaining the survival of the ischemic penumbra. This study aims to observe the labeling effects of different experimental methods on the cerebral collateral arteries of mice in vitro and in vivo. Methods: Primary (Willis circle) and secondary (leptomeningeal) collateral arteries in mice were labeled in vitro using latex perfusion, DiI perfusion, and ink-gelatin perfusion techniques. Subsequently, the diameter of these collateral arteries was meticulously measured. Specifically, the latex perfusion method was employed to compare the number of LMCs between different mouse strains. To enable stable in vivo observation of LMCs, a closed cranial window was successfully constructed. Additionally, a mouse model of distal middle cerebral artery occlusion stroke was established via electrocoagulation, followed by triphenyltetrazolium chloride (TTC) staining. For further investigation, the diameter of LMCs was continuously monitored using a fluorescence stereomicroscope, while the blood flow in the peri-infarct area was detected by laser speckle contrast imaging. Results: The latex perfusion method and DiI perfusion method can both label collateral artery vessels, but not veins. There is no significant difference in the diameter of collateral vessels measured by the latex perfusion method and DiI perfusion method (P > 0.05). The DiI perfusion method often exhibits suboptimal perfusion efficiency. The number of LMCs in C57BL/6 mice is significantly higher than that in Balb/C mice (P<0.0001). During the 3-week period of the closed cranial window, the clarity or imaging quality of the cranial window was not significantly affected. TTC staining shows the stable construction of the mice stroke model. The diameter of the LMCs increases and the blood flow in the peri-infarct area recovers after ischemic stroke (P<0.05). There is a strong positive correlation between them (P<0.05). Conclusions: Latex perfusion method can effectively label the primary and secondary collateral arteries of mice in vitro. Through fluorescence stereomicroscope and laser speckle contrast imaging, continuous observations can be made on LMCs in vivo. The remodeling of collateral vessels after ischemic stroke may promote the recovery of blood flow in the penumbra.