The thalamus is a highly connected subcortical structure that relays and integrates sensory and cortical information, which is critical for coherent and accurate perceptual awareness and cognition. Thalamic dysfunction is a classical finding in schizophrenia (SZ), and resting-state functional MRI has implicated somatomotor and frontal lobe thalamic dysconnectivity. However, it remains unclear whether these findings generalize to different psychotic disorders, are confined to specific thalamic sub-regions, and how they relate to structural thalamic alterations. Within-thalamic and thalamo-cortical functional connectivity was assessed using resting-state functional MRI data obtained from patients with SZ (n = 96), bipolar disorder (BD, n = 57), and healthy controls (HC, n = 280). Further, we used thalamic sub-regions as seeds to investigate specific cortical connectivity patterns, and performed structural analyses of thalamic volume and shape. Results showed reduced within-thalamic connectivity and thalamo-frontoparietal coupling in SZ and increased thalamo-somatomotor connectivity in BD. One thalamic sub-region showed increased sensory connectivity in SZ and eight sub-regions showed reductions with frontal and posterior areas. Reduced gray matter and shape abnormalities were found in frontal-projecting regions in both SZ and BD, but did not seem to explain reduced functional connectivity. Aberrant thalamo-cortical connectivity patterns in SZ and BD supports the notion of the thalamus as a key structure in the functional connectome across the psychosis spectrum, and the frontal and somatomotor anatomical distribution is in line with the characteristic cognitive and perceptual symptoms in psychotic disorders.