Research about the negative symptoms of chronic schizophrenia (SZ) is still lagging behind, in order to more comprehensively and systematically understand the biological and molecular mechanisms behind them, as well as to explore more valuable research directions and treatment options. By summarizing the results of previous studies and exploring them at the levels of neurobiology, genetics, molecular biology and microbiology, the authors provide a preliminary review of the new research progress in recent years. The authors hypothesize neurodevelopmental disorders by thoroughly investigating the anatomical features of various brain regions and the corresponding abnormalities in neurotransmitters. This paper then provides a relatively fresh perspective by summarizing the potential pathogenic mechanisms in terms of the brain-gut axis and metabolic syndrome. Ultimately, it is determined that the pathophysiology of chronic schizophrenia is associated with multiple biological mechanisms within the body, primarily arising from neurological abnormalities within the brain. On the basis of this, the author provides a conceptualization of the pathophysiology and a potential course of treatment.