Drought is one of the main factors affecting maize production, and development of new cultivars with high yield stability under water stress is a major breeding objective. With the enrichment of bioinformatics databases and development of genomic technology, progress on identification of the consensus drought-tolerant QTLs provide new approaches and prospects for molecular breeding of drought tolerance in maize. According to our previous study, some important constitutive and adaptive QTLs using meta-analysis were identified and to find specific genes and their families for speculating on drought tolerance networks. The objective of this study was: on the basis of excavated drought-tolerant universal QTLs, we selected 18 linked markers to develop and verify the drought tolerance in 24 different germplasms. The results were as follows: (1) 42 polymorphism sites allelic variants were detected and a mean polymorphism information content of 0.4245, with a range of 0.0799 to 0.7170. (2) By GGT32 analysis, five linked markers (including umc2217, umc2029, phi099, umc1213 and phi022) showed significant variations among different germplasms, which may be initially used to identify different drought-tolerant materials. (3) Using the analysis of chi-square test, we found that linked markers phi022 and umc2217 have reached significant levels, which might be closely related to sites of drought tolerance. Therefore, these linked markers can not only be for the corresponding groups of drought-resistant marker-assisted selection, and lay the foundation for future marker-assisted selection and drought resistance gene cloning.