Mungbean breeding objective traits are mostly controlled by multiple quantitative genes. The phenotypes of mungbean are affected by environment greatly. In order to analysis the genetic of the yield-associated traits in mungbean, RIL populations (F10) derived from the cross between an economical parent Berken and a wild parent ACC41 were planted in Beijing and Nanjing for their yield-associated agronomic traits evaluation. The results showed that in total of 63 QTLs were investigated in Beijing and Guangxi (25 in Beijing and 38 in Guangxi), located on twelve linkage groups except the 13th group. Most of the QTLs were detected in single environment, indicating the significant interactions between QTL and environments. Only 6 QTLs controlling pod length, 100-seed weight and day to mature were detected in both Beijing and Guangxi environment. Those QTLs will be of special significance for mungbean’s molecular-marker-assisted-breeding. Two regions on linkage group 5 and 9 with clustered QTLs relevant to multiple yield-associated agronomic traits and five linkage group with bundled QTLs relevant to a single agronomic traits identified in the study may provide the genetic loci of the universal yield QTL.