Organisms alter their phenotypes in response to changing environmental conditions. The developmental basis of this phenomenon, phenotypic plasticity, is a topic of broad interest in many fields of biology. While insects provide a suitable model for studying the genetic basis of phenotypic plasticity, the physiological aspects of plasticity are not fully understood. Here, we report the physiological basis of polyphenism, an extreme form of phenotypic plasticity by utilizing a dung beetle species, Onthophagus taurus. We highlighted the metabolome between sexes as well as two distinct male morphs-large and small horns. Unlike results from previous transcriptomic studies, the comparative metabolomic study revealed that differences in metabolite level were more prominent between animals with different body sizes than different sexes. Our results also indicate that specific metabolites and biochemical pathways may be active during horn size determination.