Two sets of reciprocal introgression line (IL) populations, i.e., ILs with Lemont as recurrent parent (IL_LT) and ILs with Teqing as recurrent parent (IL_TQ), were developed and evaluated for traits representing panicle size, including primary branch number (PBN), secondary branch number (SBN), and spikelet number per panicle (SNP). Together with the regression to recurrent parent by advanced backcross, transgressive segregations were observed for all traits. Correlation and regression analysis showed that SBN had much higher contribution to SNP than PBN. It was confirmed by the QTL analysis that many common loci were detected between SBN and SNP, in comparison with single common locus between PBN and SNP. One and three main effect QTLs (M-QTLs) were detected for PBN in IL_LT and IL_TQ, respectively. Six M-QTLs per trait per populations were associated with SBN and SNP. Less number and lower contribution of epistasis were detected in IL populations in comparison with mapping result from F2 or RI population. There were only four QTLs in fourteen loci (near 30%) commonly detected in both reciprocal IL populations implying the large impact of genetic background on QTLs expression.