Abstract Optical coherence tomography (OCT) is a non-invasive imaging technique that generates cross-sectional images of biological tissues at millimeter-level penetration depth with micron-level resolution. In this study, we developed a custom spectral-domain OCT system equipped with a flash stimulus module for dual-modality imaging of mouse retinal structure and function. The axial resolution of the system reached ∼2.7/2 μm in air/tissue following optimization and calibration. We deployed this system to conduct in vivo OCT structural imaging and optoretinography (ORG) functional assessment of mouse retina to investigate the effects of three anesthesia regimens. Statistical analysis of the results indicates that anesthesia results in a smaller relative intensity of inner/outer segment junction and external limiting membrane and a thickening of the outer segment compared to an awake state. Meanwhile, significant differences were observed in the effects on retinal structure and function between isoflurane and tribromoethanol anesthesia, while differences between isoflurane and esketamine+xylazine groups were small. These findings suggest that the type of anesthetic should be taken into account when comparing imaging results across studies reported in the literature.