Abstract Background and Hypothesis Schizotypy has been conceptualized as a continuum of symptoms with marked genetic, neurobiological, and sensory-cognitive overlaps to schizophrenia. Hierarchical organization represents a general organizing principle for both the cortical connectome supporting sensation-to-cognition continuum and gene expression variability across the cortex. However, a mapping of connectome hierarchy to schizotypy remains to be established. Importantly, the underlying changes of the cortical connectome hierarchy that mechanistically link gene expressions to schizotypy are unclear. Study Design The present study applied novel connectome gradient on resting-state fMRI data from 1013 healthy young adults to investigate schizotypy-associated sensorimotor-to-transmodal connectome hierarchy and assessed its similarity with the connectome hierarchy of schizophrenia. Furthermore, normative and differential postmortem gene expression data were utilized to examine transcriptional profiles linked to schizotypy-associated connectome hierarchy. Study Results We found that schizotypy was associated with a compressed functional connectome hierarchy. Moreover, the pattern of schizotypy-related hierarchy exhibited a positive correlation with the connectome hierarchy observed in schizophrenia. This pattern was closely colocated with the expression of schizophrenia-related genes, with the correlated genes being enriched in transsynaptic, receptor signaling and calcium ion binding. Conclusions The compressed connectome hierarchy suggests diminished functional system differentiation, providing a novel and holistic system-level basis for various sensory-cognition deficits in schizotypy. Importantly, its linkage with schizophrenia-altered hierarchy and schizophrenia-related gene expression yields new insights into the neurobiological continuum of psychosis. It also provides mechanistic insight into how gene variation may drive alterations in functional hierarchy, mediating biological vulnerability of schizotypy to schizophrenia.