Fertile spikelet number per spike (FSN) and grain number per fertile spikelet (GNFS) contribute greatly to wheat yield improvement. To detect quantitative trait loci (QTL) associated with FSN and GNFS, a recombinant inbred line (RIL) population derived from the cross of Zhongkemai 13F10 and Chuanmai 42 was employed across eight environments. Two Genomic regions associated with FSN were detected on chromosomes 2A and 6A using bulked segregant exome sequencing (BSE-Seq) analysis. Based on the constructed genetic linkage map, four QTL QFsn.cib-2A, QFsn.cib-6A, QGnfs.cib-2A and QGnfs.cib-6A were identified in three or more environments. Among them, two major QTL QFsn.cib-2A (LOD=4.67–9.34, PVE=6.66–13.05%) and QGnfs.cib-2A (LOD=5.27–11.68, PVE=7.95–16.71%) were detected in seven and six environments, respectively. They were co-located in the same region, namely QFsn/Gnfs.cib-2A . This locus was further verified by the linked Kompetitive Allele Specific PCR (KASP) markers in a different genetic background. QFsn/Gnfs.cib-2A showed pleiotropic effects on grain number per spike (GNS) and spike compactness (SC) and had no effect on grain weight. Since QFsn/Gnfs.cib-2A might be a new locus, it and the developed KASP markers can be used in wheat breeding. According to haplotype analysis, QFsn/Gnfs.cib-2A was identified as a target of artificial selection during wheat improvement. Based on haplotype analysis, sequence differences, spatiotemporal expression patterns and gene annotation, TraesCS2A03G0978700 was predicted as the potential candidate gene for QFsn/Gnfs.cib-2A . These results provide valuable information for fine mapping and cloning gene(s) underlying QFsn/Gnfs.cib-2A.