This study explored the alterations of gut microbiome in a cohort of adult patients with craniopharyngioma using the high-throughput sequencing of 16S rRNA gene sequencing and metagenomics approaches. In addition, high performance liquid chromatography-mass spectrometry (HPLC-MS) was utilized to explore the differences in serum metabolites between healthy individuals and adult patients with craniopharyngioma. The first dataset illustrated the basic informations of all participants enrolled in 16S rRNA sequencing and metagenomic sequencing study along with clinical indices of all patients. The second dataset demonstrated the basic informations of participants in serum metabolomics study and concentrations of all detected metabolites.