In the study, ten panicle traits associated with yield sink size were measured in a recombinant inbred population derived from Zhenshan 97 x Minghui 63. Generally, spikelets per panicle were more closely correlated with number of secondary branch per panicle, spikelets on secondary branch per secondary branch, and spikelet density. A total of 53 QTL were detected for ten traits in two years. Approximately 43.4% QTLs were detected in both two years, suggesting environmental effects on traits. Five chromosomal regions (G359-RG532 and C567-C86-RG236 on chromosome 1, R712-RM29 on chromosome 2, P-RG424 on chromosome 6, C148-RM258 on chromosome 10) were detected to have effects on multiple panicle traits. QTLs for traits, which were correlated, were generally localized in similar chromosomal regions, suggesting that pleiotropy and (or) linkage are the molecular basis of relationship between them. A large number of digenic interactions were detected, 18.2% of which were detected simultaneously in both two years. The proportion of common interactions was trait-depended, ranging 8.7% for spikelets on secondary branch per secondary branch to 32.6% for panicle length. Approximately 26.7% of common two-locus combinations had pleiotropic effects by simultaneously influencing two or more traits. Overall, the results indicate that each panicle trait is controlled by several QTLs, genotype x environment interaction, and a large number of epistatic interactions.