The elongation of mesocotyl plays a crucial role in the emergence of maize seedlings, but the genetic mechanisms that control mesocotyl elongation remain largely unknown. In this study, we investigated the mesocotyl lengths of a maize association panel containing 364 inbred lines. Through genome-wide association analysis, we mapped and cloned ZmCCT11, a transcription factor of the CCT family that is localized in the nucleus and possesses transcriptional transactivation activity. Knocking out the expression of ZmCCT11 via the CRISPR/Cas9 approach reduced, while overexpression of this gene promoted maize mesocotyl length. Further studies showed that ZPUM5 (an RNA-binding protein) inhibited the protein accumulation of ZmCCT11 by binding to the “UGUA” motifs in the 3’UTR of ZmCCT11, and zpum5 mutants showed a longer mesocotyl, similar to the ZmCCT11-OE lines. Transcriptomic analysis showed that ZmCCT11 may promote mesocotyl elongation by up-regulating the expression of genes involved in the auxin signaling pathway. Based on the SNPs, which are significantly associated with maize mesocotyl length, the maize inbred lines were classified into ZmCCT11typeA and ZmCCT11typeB with ZmCCT11typeA is favorable for promoting mesocotyl elongation. Further analysis found that the ZmCCT11typeA allele emerged sequentially after the domestication of maize and was selected for higher altitude adaptation of maize. Our studies demonstrate the genetic mechanisms of maize mesocotyl elongation, and provide new genetic resources and molecular markers for breeding deep-sowing-tolerant maize cultivars.