To date, large amounts of genomic and phenotypic data have been accumulated in the fields of crop genetics and genomic research, and the data are increasing very quickly. However, the bottleneck to using big data in breeding is integrating the data and developing tools for revealing the relationship between genotypes and phenotypes. Here, we report a rice sub-database of an integrated omics knowledgebase (MBKbase-rice, www.mbkbase.org/rice), which integrates rice germplasm information, multiple reference genomes with a united set of gene loci, population sequencing data, phenotypic data, known alleles and gene expression data. In addition to basic data search functions, MBKbase provides advanced web tools for genotype searches at the population level and for visually displaying the relationship between genotypes and phenotypes. Furthermore, the database also provides online tools for comparing two samples by their genotypes and finding target germplasms by genotype or phenotype information, as well as for analyzing the user submitted SNP or sequence data to find important alleles in the germplasm. A soybean sub-database is planned for release in 3 months and wheat and maize will be added in 1–2 years. The data and tools integrated in MBKbase will facilitate research in crop functional genomics and molecular breeding.