In arid or semi-arid regions, deep-sowing is an effective treasure to ensure seeds absorbing water from deep soil layer at present. However, the existing maize varieties have poor tolerance to deep-sowing, which is attributed to that few genes are explored and utilized. In this study, 243 IBM Syn4 recombinant inbred lines (RIL) constructed with B73 and Mo17 as parents, and 1339 DNA markers evenly distributed in 10 chromosomes, were used for QTL analysis of deep-sowing tolerance during seed germination. There were significant differences in germination-related traits between the parental lines at 12.5 cm sowing depth. Among them, 7, 7, 5, 10, 2 QTLs for emergence rate, seedling length, plumule length, mesocotyl length, coleoptile length were detected, respectively. These QTLs explained 2.75% to 10.49% of the phenotypic variance with LOD scores ranging from 2.50 to 8.27. In addition, 12 overlapping QTLs formed 5 QTL clusters on chromosome 3, 5, 7, 9. This study provides a basis for molecular marker assisted breeding and functional study in deep-sowing germination of maize.