Copy numbers of homologous gene families vary greatly among different species, which is caused by the differences in the rates of gene gain and loss. It is well known that gene copy number variation can be responsible for the phenotypic novelties of particular species. In this study, 64 species that represent the main vertebrate groups spanning evolutionary period of about 600 million years were selected and the homology of gene families across these species were established, thereby revealing the evolutionary patterns of gene family size in vertebrates. The results show that among the 6857 gene families inferred to be present in the most recent common ancestor of the vertebrates, 6712 had changed their sizes in at least one lineage, and these gene families had contracted in most cases. Gene families in Choloepus hoffmanni and Danio rerio had undergone the greatest contraction and expansion, respectively. Based on the highly dynamic evolution of vertebrate gene family size, we sought to identify any genomic signals that might be related to the evolution of specific vertebrate populations from the perspective of the distinct gene family size changes. We observed a high proportion of gene family amplification occurred, probably due to genome-wide duplication in the recent common ancestral genome of teleosts, which was followed by contraction in the decedents due to the extensive gene fractionation. Furthermore, we found evidence that orphan genes in the bony fish might contribute to the adaptive evolution of fish in aquatic environment. For example, some orphan genes were involved in fin development, tail development and kidney physiology. Overall, our work provides novel insights into the evolution of vertebrate gene family size and provides several lines of evidence for understanding the relationship between the genome evolution and phenotypic diversity in vertebrates.