Phylogenomic approaches are growingly applied in the systematic studies of animals with the rapid advancement of sequencing and analytical tools. Aiming to accelerate the systematic studies using genome-scale data in China, this paper outlines the commonly used techniques for generating phylogenomic datasets: RNA-seq based transcriptome, target-enrichment based UCEs and AHE, RAD-seq, whole genome sequencing, and briefly discusses the pros and cons of each technique. Major analytical procedures for the 1KITE transcriptome pipeline, the PHYLUCE (UCEs) and AHE pipelines and the PLWS (low-coverage whole genome sequencing) pipeline are summarized, and recent achievements valuable for phylogenomic analyses are introduced.