MaizeCUBIC is a free database that describes genomic variations, gene expression, phenotypes and quantitative trait locus (QTLs) for a maize CUBIC population (24 founders and 1404 inbred offspring). The database not only includes information for over 14M single nucleotide polymorphism (SNPs) and 43K indels previously identified but also contains 660K structure variations (SVs) and 600M novel sequences newly identified in the present study, which represents a comprehensive high-density variant map for a diverse population. Based on these genomic variations, the database would demonstrate the mosaic structure for each progeny, reflecting a high-resolution reshuffle across parental genomes. A total of 23 agronomic traits measured on parents and progeny in five locations, where are representative of the maize main growing regions in China, were also included in the database. To further explore the genotype-phenotype relationships, two different methods of genome-wide association studies (GWAS) were employed for dissecting the genetic architecture of 23 agronomic traits. Additionally, the Basic Local Alignment Search Tool and primer design tools are developed to promote follow-up analysis and experimental verification. All the original data and corresponding analytical results can be accessed through user-friendly online queries and web interface dynamic visualization, as well as downloadable files. These data and tools provide valuable resources on genetic and genomic studies of maize and other crops.