Ischemic stroke (IS) is characterized by the sudden interruption of blood supply to the brain, resulting in neurological impairments and even mortality. Photoacoustic computed tomography (PACT) integrates the high contrast of optical imaging and the penetration of ultrasound imaging, enabling non-invasive IS evaluation. However, the image reconstruction quality significantly affects the oxyhemoglobin saturation (sO2) estimation. This study investigates a model-based with total variation minimized by augmented Lagrangian and alternating direction (MB-TVAL3) approach and compared it with the widely used back-projection (BP) and delay-and-sum (DAS) algorithms. Both simulations and invivo experiments are conducted to validate the performance of the MB-TVAL3 algorithm, showing a higher sO2 estimation accuracy and sensitivity in detecting infarct area compared to BP and DAS. The findings of this study emphasize the impact of acoustic inverse problem on the accuracy of sO2 estimation and the proposed approach offers valuable support for IS evaluation and cerebrovascular diagnosis.