The progress of schizophrenia at various stages is an intriguing question, which has been explored to some degree using single-modality brain imaging data, e.g. gray matter (GM) or functional connectivity (FC). However it remains unclear how those changes from different modalities are correlated with each other and if the sensitivity to duration of illness and disease stages across modalities is different. In this work, we jointly analyzed FC, GM volume and single nucleotide polymorphisms (SNPs) data of 159 individuals including healthy controls (HC), drug-naive first-episode schizophrenia (FESZ) and chronic schizophrenia patients (CSZ), aiming to evaluate the links among SNP, FC and GM patterns, and their sensitivity to duration of illness and disease stages in schizophrenia. Our results suggested: 1) both GM and FC highlighted impairments in hippocampal, temporal gyrus and cerebellum in schizophrenia, which were significantly correlated with genes like SATB2, GABBR2, PDE4B, CACNA1C etc. 2) GM and FC presented gradually decrease trend (HC > FESZ > CSZ), while SNP indicated a non-gradual variation trend with un-significant group difference observed between FESZ and CSZ; 3) Group difference between HC and FESZ of FC was more remarkable than GM, and FC presented a stronger negative correlation with duration of illness than GM (p = 0.0006). Collectively, these results highlight the benefit of leveraging multimodal data and provide additional clues regarding the impact of mental illness at various disease stages.