Serum glucose and lipids are important indicators for host metabolic condition. Interaction of host and gut microbes regulates the metabolism process. However, how much the gut microbiome contributes to the variance of serum glucose and lipids is largely unknown. Here we carried out a 16S rRNA gene based association study between cecum microbiome and the concentration of serum glucose and lipids in 240 Chinese Erhualian pigs. We identified tens of bacterial taxa associated with serum glucose and lipids. The butyrate-producing bacteria were significantly associated with serum glucose level. The pathogenic bacteria belonging to Proteobacteria and Fusobacteria showed significant associations with increased serum lipid levels, while the bacteria Lactobacillus and Bacilli had negative correlations with serum lipids. Cross-validation analysis revealed that 23.8% variation of serum glucose and 1.6%~6.0% variations of serum lipids were explained by gut microbiome. Furthermore, predicted function capacities related to nutrition intake, transport and carbohydrate metabolism were significantly associated with serum glucose level, while the pathways related to antioxidant metabolism and bile synthesis tended to be associated with serum lipid level. The results provide meaningful information to get insight into the effect of gut microbiome on serum glucose and lipid levels in pigs.