A better understanding of wheat functional genomics can improve targeted breeding for better agronomic traits and environmental adaptation. However, the lack of gene-indexed mutants and low transformation efficiency in wheat limits in-depth gene functional studies and genetic manipulation for breeding. In this study, we created a library of KN9204, a popular wheat variety in northern China, with a reference genome, transcriptome, and epigenome of different tissues, using ethyl methyl sulfonate (EMS) mutagenesis. This library contains a vast developmental diversity of critical tissues and transition stages. Exome capture sequencing of 2,090 mutant lines, using KN9204 genome-designed probes revealed that 98.79% of coding genes had mutations, and each line had an average of 1,383 EMS-type SNPs. We identified new allelic variations for crucial agronomic trait-related genes, such as Rht-D1, Q, TaTB1, and WFZP. We tested 100 lines with severe mutations in 80 NAC TFs under drought and salinity stresses and identified 13 lines with altered sensitivity. Further analysis of three lines using transcriptome and chromatin accessibility data revealed hundreds of direct targets of NAC with altered transcriptional patterns under salt or drought stress, including SNAC1, DREB2B, CML16, and ZFP182, factors known to respond to abiotic stress. Thus, we have generated and indexed KN9204 EMS mutant library, which would facilitate functional genomics research and offer resources for genetic manipulation in wheat.