The clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein (Cas) genome editing system (CRISPR-Cas) is revolutionizing agriculture. As the efficiency of CRISPR-Cas largely determined by the specificity of gRNA and the chromatin status of target region, a gRNA design tool that quickly scans the genome for on-targets and off-targets, and considers chromatin accessibility at target region is highly demanded for gene editing and molecular breeding, especially for wheat with a gigantic genome. Here, we developed CRISPR-Cereal, a fast and flexible gRNA web design tool for wheat, maize and rice. CRISPR-Cereal not only provides the predicated on-targets and genome-wide off-targets with maximum five mismatches of candidate gRNAs, but also integrates regulome information including gene expression, chromatin accessibility, histone modification and DNA methylation of the target regions to promote precise and high-efficient gene editing. For application of CRISPR-Cas9 system in practical breeding of the three major cereal crops, CRISPR-Cereal considers single nucleotide polymorphisms (SNPs) existed in the candidate gRNAs. CRISPR-Cereal is freely available at http://crispr.hzau.edu.cn/CRISPR-Cereal/.