<b><i>Introduction:</i></b> Observational studies highlight associations of common diseases with individual schizophrenia symptoms. However, it is unclear whether these diseases are associated with individual treatment-resistant schizophrenia (TRS). We aimed to explore the genetic associations between common immune diseases, metabolic diseases, psychiatric disorders, gut microbiota and TRS. <b><i>Methods:</i></b> Genome-wide association study (GWAS) summary data of European participants (<i>n</i> = ∼456,327) included TRS, 11 psychiatric disorders, 23 immune and metabolic diseases, body mass index, height, and 211 gut microbiota. In this genetic correlation and two-sample Mendelian randomization (MR) study, linkage disequilibrium score (LDSC) regression was applied to infer genetic correlation estimates. Two-sample MR tested potential causal associations of genetic variants associated with common immune diseases, metabolic diseases, psychiatric disorders, and gut microbiota with TRS. <b><i>Results:</i></b> LDSC revealed candidate associations between attention deficit/hyperactivity disorder (ADHD), schizophrenia, intestinal infectious diseases, obesity and TRS (genetic correlation range, 0.230–0.702; <i>p</i> < 0.05). Two-sample MR analyses suggested that ADHD was positively associated with TRS (estimate [SE] = 0.204 [0.073], <i>p</i> = 0.005), a finding that remained stable across statistical models. Besides, schizophrenia and <i>genus Barnesiella</i> levels were causally associated with TRS but not consistent across MR approaches. <b><i>Conclusion:</i></b> This study reports genetic correlations between ADHD, schizophrenia, intestinal infectious diseases, obesity and TRS. The study also found that <i>genus Barnesiella</i> was associated with TRS. These findings may have clinical implications, highlighting the possible strategy for TRS prevention.