Combining ability is essential for hybrid breeding in crops. However, the genetic basis of combining ability remains unclear and has been seldom investigated. Identifying molecular markers associated with this complex trait would help to understand its genetic basis and provide useful information for hybrid breeding in maize. In this study, we identified genetic loci of general combining ability (GCA) and specific combining ability (SCA) for five yield-related traits under three environments using a set of testcrosses with introgression lines (ILs). GCA or SCA of the five yield-related traits of the ILs was estimated by the performance of testcrosses with four testers from different heterotic groups. Genetic correlations between GCA of the traits and the corresponding traits per se were not significant or not strong, suggesting that the genetic basis between them is different. A total of 56 significant loci for GCA and 21 loci for SCA were commonly identified in at least two environments, and only 5 loci were simultaneously controlling GCA and SCA, indicating that the genetic basis of GCA and SCA is different. For all of the traits investigated, positive and significant correlations between the number of GCA loci in the ILs and the performance of the corresponding GCA of the ILs were detected, implying that pyramiding GCA loci would have positive effect on the performance of GCA. Results in this study would be useful for maize hybrid breeding.