The genetic mechanism underlying panicle number per plant (PN), spikelet number per panicle (SNP) and its related traits in rice was analysed using 292 F13 RILs from the cross of Lemont/Teqing and a complete linkage map with 272 molecular markers. The RILs showed tremendous transgressive segregation for all traits studied. The weak negative correlation between PN and SNP was observed. Fifty-one QTLs and 45 epistatic QTL pairs affecting these traits were identified, collectively explaining over 60% of the total variation of individual traits. Almost all SNP-QTLs were attributable to one or more of its contributing components. Branching number traits had greater contributions to SNP than length traits, in which the first had twice as many QTLs mapped in the same or near regions with SNP as the latter. Only two PN-QTLs were mapped in the near regions with those of related traits of SNP, suggesting a reasonable recombination between PN and SNP would be available by marker-assisted selection (MAS). Some major QTLs including QPn4 for panicle number, QPbn3a, QPbn3b and QPbl4 for panicle branching and length would be of great value in MAS. It was discussed that a new high-yielding panicle type was resulted from reasonably deploying for QTLs of panicle traits by MAS.