Yeasts are known to have versatile metabolic traits, while how these metabolic traits have evolved has not been elucidated systematically. We performed integrative evolution analysis to investigate how genomic evolution determines trait generation by reconstructing genome‐scale metabolic models (GEMs) for 332 yeasts. These GEMs could comprehensively characterize trait diversity and predict enzyme functionality, thereby signifying that sequence‐level evolution has shaped reaction networks towards new metabolic functions. Strikingly, using GEMs, we can mechanistically map different evolutionary events, e.g. horizontal gene transfer and gene duplication, onto relevant subpathways to explain metabolic plasticity. This demonstrates that gene family expansion and enzyme promiscuity are prominent mechanisms for metabolic trait gains, while GEM simulations reveal that additional factors, such as gene loss from distant pathways, contribute to trait losses. Furthermore, our analysis could pinpoint to specific genes and pathways that have been under positive selection and relevant for the formulation of complex metabolic traits, i.e. thermotolerance and the Crabtree effect. Our findings illustrate how multidimensional evolution in both metabolic network structure and individual enzymes drives phenotypic variations. Synopsis: A large‐scale systematic evolution analysis, metabolic model reconstruction and simulation are used to examine the evolutionary mechanism underlying the emergence of diverse traits across 332 different yeast species. Reconstruction and comparative analysis of 332 yeast species‐specific genome‐scale metabolic models allows refining gene function annotation and characterizing unclear substrate utilization pathways.Metabolic network expansion through gene duplication and enzyme promiscuity drives trait gains in substrate utilization.Gaps in downstream pathways can result in trait losses.Integrative analyses show that positive selection of genes in amino acid and protein synthesis sub‐pathways is relevant for the emergence of thermotolerance in yeast. [ABSTRACT FROM AUTHOR]