Many paleognaths (ratites and tinamous) have a pair of homomorphic ZW sex chromosomes in contrast to the highly differentiated sex chromosomes of most other birds. To understand the evolutionary causes for different tempo of sex chromosome evolution, we produced female genomes of 12 paleognathous species and reconstructed the phylogeny and the evolutionary history of paleognathous sex chromosomes. We uncovered that Palaeognathae sex chromosomes had undergone stepwise recombination suppression and formed a pattern of ‘evolutionary strata’. Nine of the 15 studied species’ sex chromosomes have maintained homologous recombination in their long pseudoautosomal regions extending over half of the entire chromosome length. We found that in older strata, the W-chromosome suffered more serious functional gene loss. Their homologous Z-linked regions, compared to other genomic regions, have produced an excess of species-specific autosomal duplicated genes that evolved female-specific expression, in contrast to their broadly-expressed progenitors. We speculate the ‘de-feminization’ of Z chromosome with underrepresentation of female-biased genes and slow divergence of sex chromosomes of paleognaths might be related to their distinctive mode of sexual selection targeting females that evolved in their common ancestors.