Beyond causing local injury, stroke disrupts structural and functional organization of the brain networks, exposing patients to a high risk of cognitive impairment by affecting the neural network activity. However, the impact of these pathological changes on cognition-related neural circuits is not well understood. In this study, we mainly focused on structures and directed functional connectivity within the Papez circuit in subacute stroke patients. Forty-five stroke patients and thirty-four age-, sex-matched healthy controls were included in our study. The Papez circuit gray matter were measured to explore ischemia-induced structural alterations. And Granger causality analysis with the hippocampus as seed regions was performed to identify alterations of directional functional connectivity within the neural circuit. We also explored the associations between cerebral changes with cognitive status. Compared with healthy controls, stroke patients revealed marked atrophy in gray matter of the Papez circuit, including ipsilateral hippocampus, amygdala, thalamus, and caudal anterior cingulate gyrus. Additionally, there are alterations in the directed functional connections between the bilateral hippocampus and cingulate gyrus within the Papez circuit. These altered effective connectivities were correlated with cognitive function after cerebrovascular event. Taken together, in the early post-stroke period, disruptions of the Papez circuit in both architecture and directed functional connectivity have already occurred and might affect the cognitive function. These findings have prompted researchers to better understand the potential mechanisms underlying vascular cognitive impairment and to investigate new therapeutic targets that could reduce cognitive burden.