Flag leaf, which is a major sink organ of rice plant, was reported to significantly positive correlate with the grain yield. Illustrating the genetic basis of flag leaf related traits and the grain yield is of significance in breeding for high-yield varieties with ideal plant type. In the present study, a diverse panel of 1016 rice accessions was evaluated for flag leaf related traits including flag leaf length (FLL), flag leaf width (FLW), flag leaf area (FLA), as well as the grain yield per plant (GY) in Jingzhou of Hubei province in two calendar years (2015 and 2016). The abundant variations at four traits were observed within this population, but the phenotypic variations were found to be largely environmental-dependent. The correlations between GY and each of FLL, FLW, FLA were low.Using genome-wide association analysis based on 4.8M high throughput SNP datasets, a total of 31 QTL for flag leaf related traits and GY were identified. Especially, one QTL (qFLW4) for FLW was detected in both two calendar years. Three regions were found to be associated with two traits including qFLW4 and qFLA4 for FLW and FLA, qFLL6 and qFLA6 for FLL and FLA, and qFLL10 and qFLA10 for FLL and FLA. Using haplotype and bioinformatic analyses in QTL regions, seven candidate genes and 10 favorable alleles were identified. Taken together, our results provided a preliminary base in order to clone the functional genes underlying rice flag leaf related traits, and breed for elite rice varieties with an ideal plant type by deploying different favorable genes by marker-assisted selection.