Deep-sowing is an important method for avoiding drought stress in crop species, including maize. Identifying candidate genes is the groundwork for investigating the molecular mechanism underlying maize deep-sowing tolerance. This study evaluated four traits (mesocotyl length at 10 and 20 cm planting depths and seedling emergence rate on days 6 and 12) related to deep-sowing tolerance using a large maize population containing 386 inbred lines genotyped with 0.5 million high-quality single nucleotide polymorphisms (SNPs). The genome-wide association study detected that 273 SNPs were in linkage disequilibrium (LD) with the genetic basis of maize deep-sowing tolerance. The RNA-sequencing analysis identified 1944 and 2098 differentially expressed genes (DEGs) in two comparisons, which shared 281 DEGs. By comparing the genomic locations of the 273 SNPs with those of the 281 DEGs, we identified seven candidate genes, of which GRMZM2G119769 encoded a sucrose non-fermenting 1 kinase interactor-like protein. GRMZM2G119769 was selected as the candidate gene because its homologs in other plants were related to organ length, auxin, or light response. Candidate gene association mapping revealed that natural variations in GRMZM2G119769 were related to phenotypic variations in maize mesocotyl length. Gene expression of GRMZM2G119769 was higher in deep-sowing tolerant inbred lines. These results suggest that GRMZM2G119769 is the most likely candidate gene. This study provides information on the deep-sowing tolerance of maize germplasms and identifies candidate genes, which would be useful for further research on maize deep-sowing tolerance.