New materials are the basis and premise of breeding elite maize hybrids. This study was based on the scanning with MaizeSNP50 BeadChip (containing 60,000 SNPs) of the whole genome of 104 test materials that included tropical/subtropical germplasms, temperate-tropical lines (SI, PB, etc.), Reid, Lancaster and Tangsipingtou groups, and on the analysis with R language package GAPIT of the population genetic structure. Improved lines QB5721, QB5722, QB5744, QB5725, QB5775, QB5785 from SI (Suwan-Iodent) populations, representative line HCL645 of Iodent germplasm, and tropical Suwan germplasms QR273, ZH908 were chosen as the materials, with Iodent and 6 improved lines paired with 7 test materials from different groups to obtain 49 cross combinations, according to NCII design. Heterosis of the 6 SI lines was evaluated by RGCA (relative effect of general combining ability) of grain weight per spike. Analysis of genetic structure based on MaizeSNP50 BeadChip scanning divided the 104 materials into four types: tropical germplasm, Tangsipingtou (TSPT), Reid-Lancaster, and Iodent germplasm. The genetic distance was large between Iodent group and other five types of germplasm, and SI germplasm improved lines were clearly superior to Reid, Lancaster, and PB groups in heterosis. Phenotypic analysis indicated that the range of RGCA of the 6 SI improved lines was between ?1.62% and 5.67%, and the range of RSCA (relative effect of specific combining ability) of the 49 cross combinations was between ?2.64% and 2.98%. The RGCA of QB5725 was 5.67%, higher than that of QB5775 (4.39%), QB5721 (2.42%), QB5722 (1.68%), QB5744 (2.29%) and HCL645 (2.38%). These results may provide new research ideas for the creation and application of tropical maize germplasm resources in temperate regions in China.