Schizophrenia (SZ) is a highly heritable disease exhibiting substantial structural and functional brain impairments. The duration of illness and medication use may cause different presentations of impairments in patients. To understand the progressive variations of the disease, most recent studies have reported brain functional or structural abnormalities associated with illness duration, but a comprehensive study of pathology underlying brain structure, function and illness duration is still limited. In this work, we employed a three-way parallel independent component analysis (pICA) algorithm to jointly analyze grey matter volume(GM), functional connectivity (FC) and single nucleotide polymorphisms (SNPs) from drug-naïve first-episode [FESZ], chronic schizophrenia [CSZ]) and healthy controls[HC], aiming to identify the linked alterations in SNP-GM-FC components, and evaluate the impairment speed of imaging measures associated with SZ-susceptible genetic variants in different disease stages (FESZ and CSZ). Results demonstrated significant group differences on GM and FC in hippocampus, temporal gyrus and cerebellum between SZ and HC, which are also significantly correlated with SNPs residing in genes like GABBR2, SATB2, CACNA1C, PDE4B, involved in pathways of cell junction, synapse and neuron projection. Moreover, two-sample t-tests showed that GM volume and FC strength presented similar trends of progressive decrease with the increase of the illness duration (HC>FESZ>CSZ). Besides that genetic-related GM and FC components both showed significant associations with illness duration, FC indicates the higher impairment speed than GM, suggesting that functional connectivity may serve as a more sensitive measure to detect the disruptions in SZ at the very early stage.