In recent decades, next-generation sequencing (NGS) was developed and brought biology into a new era. Rice, maize, wheat, sorghum and barley are the most important cereal crops and feed most of the world's population. Great progress in the study of cereal genomes has been made with the help of NGS. Reference genome sequence assembly and re-sequencing have grown exponentially. Thus, evolution and comparative genomics are renewed, including origin verification, evolution tracking and so on. In this review, we briefly record the development of sequencing technology, the comparison of next-generation sequencing methods and platforms and summarize the bioinformatics tools used for NGS data analysis. We describe how NGS accelerates reference genome assembly and new evolutionary findings. We finally discuss how to discover more valuable resources and improve cereal breeding in the future.