Although functional ecology is a well-established field, our understanding of the evolutionary and ecological significance of the reproductive traits in macrofungi is still limited. Here, we reconstructed a phylogeny tree of gomphoid fungi in the narrower sense, including the species of the generaGomphusandTurbinellusand used it to uncover the evolution of reproductive traits. Our analyses indicated that fungal fruit bodies and spores did not enlarge at a steady rate over time. Early gomphoid fungi essentially maintained their fruit body size, spore size and spore shape through the Mesozoic. In the Cenozoic, gomphoid fungi acquired significantly larger and more spherical spores by simultaneously expanding in length and width, with the fruit body size first decreasing and then enlarging. We argue that these trade-offs were driven by the effect of biological extinction and the dramatic climate changes of the Cenozoic. Gomphoid fungi initially increased in spore size and fruit body number as extinction survivors filled vacant niches. Both fruit bodies and spores eventually became larger as ecosystems saturated and competition intensified. One new species ofGomphusand nine new species ofTurbinellusare described.