Facial skin is more exposed to the outside environment, and it is usually affected by environmental factors. Characterization of the skin microbiome and metabolome of individuals from different geographic regions will help to understand the factors behind the prevalence of skin disorders and support skincare product development. In the current study, volunteers from northern, southern, and northwestern China were recruited. Facial skin samples were collected for amplicon sequencing and metabolomic liquid chromatography-mass spectrometry (LC-MS/MS) analyses. We demonstrated significant alterations in the abundances of multiple microorganisms and skin lipid compositions between individuals. People living in the northwest, which has a dry climate and high altitude, showed lower level of total lipids, and lower abundance of Malassezia, but higher levels of ceramides and fatty acids. Malassezia had a positive correlation with eicosanoids and a negative correlation with ceramides. This work highlights the effects of geographic factors on the skin microbial structures and skin lipids.IMPORTANCECharacterization of the skin microbiome and metabolome across geography will help uncover the climate factors behind the prevalence of skin disorders and provide suggestions for skincare products for people living in different geographic regions. Characterization of the skin microbiome and metabolome across geography will help uncover the climate factors behind the prevalence of skin disorders and provide suggestions for skincare products for people living in different geographic regions.