Understanding the evolutionary relationships among species is fundamental to biology, not only as an account of speciation events but also as the basis for comparative analyses of trait evolution. However, the deep branches of the Neoaves, which encompass 95% of extant bird species, have been subject of numerous phylogenetic hypotheses. The reason for the complexity of resolving these branches is thought to be grounded in the explosive diversification of early Neoaves that all major groups of birds in this lineage formed within just 15 million years near the Cretaceous-Paleogene (K-Pg) boundary, ca. 66 million years ago. Since 2010, we have initiated the phylogenomic effort to resolve the deep phylogeny of birds using the full genome data. This effort has led to the further initiation of Bird Genome 10K (B10K) consortium, which aims to sequence the genome of all extant bird species and conduct the phylogenomic study for understanding the evolution and diversification of birds. Using the genomes of 363 bird species representing 92% of bird families generated from B10K, we presented a well-supported tree resolving the major debates of the deep phylogeny in early neoaves, providing a backbone tree for the future comparative and ecological studies of birds. However, we also observed some nodes remain recalcitrant due to complex evolutionary events or other reasons, and widespread incongruences in evolutionary history across bird genomes, offering fresh insights into the impacts of rapid radiation on the modern bird genomes. These rich genomic data also provide unprecedented resource for understanding the recent evolutionary history of each bird species. By comparing the demographic histories of each bird species over the past million years, we identified direct and indirect effects of key life historical traits on long-term demographic responses to climate change. With more species will be soon generated by B10K, such analyses across the tree of life will provide unique insight into the natural variability of long-term demography, and help direct conservation efforts towards species more sensitive to broad-scale global environmental change.