Based on the piling reports of disruptions in the thalamus of patients with schizophrenia, the alteration in the thalamo-cortical system has been regarded as the core pathophysiology. As the thalamus is composed of distinctive nuclei with different cytoarchitecture and cortical connections, nuclei specific investigations have been actively conducted in post-mortem studies. In addition, the importance of early changes has been highlighted, which in turn has led to investigations of the thalamo-cortical system using non-invasive neuroimaging methods. From this perspective, the early structural changes in the thalamo-cortical system, such as the thalamo-cortical connection and nuclei specific microstructural changes (which are coherent with findings from post-mortem methods) will be briefly discussed. The main findings, which are the reduced thalamo-prefrontal connection and reduced microstructural complexity in the higher-order nuclei detected in first-episode psychosis patients, suggest the occurrence of early alterations within and between the communication hub of the brain and cortex. These findings suggest not only directions for further studies for unveiling the thalamo-cortical system related pathophysiology, but also the possibility of using the reduced microstructural complexity in the higher order nucleus as a biomarker for schizophrenia.