Background: Triticum aestivum, or common wheat, is a globally important cereal crop. Alternative splicing (AS) is an important post-transcriptional regulation mechanism in higher eukaryotes, but the knowledge of AS in wheat is limited at present. Results: In this study, we performed AS mapping from the elite, high-yielding wheat cultivar Xiaoyan 6. We identified 18,960 and 25,133 novel protein-coding genes and transcript models that were not annotated in the draft genome of wheat cultivar Chinese Spring. We also found that 18,868 genes were alternatively spliced, and classified four major AS types, including alternative acceptor sites (AA), intron retention (IR), alternative donor sites (AD), and exon skipping (ES). Further analysis determined that differences in the AS frequency and AS types displayed a positive correlation with exon number and intron length and were negatively correlated with the GC content, but were not correlated with gene transcriptional level. Furthermore, we identified 2,737 seed-specific AS genes in wheat cultivar Xiaoyan 6, and demonstrated that the number of AS genes in the grain decreased with seed development, suggesting that the earlier developmental stages are more important and complex than are the later stages. In addition, the grain-specific AS genes that were ubiquitously significantly up-regulated during seed development were associated with metabolism-related pathways, indicating that AS of metabolism-related genes is crucial for grain filling in wheat. Conclusions: Through transcriptome analysis, over ten thousand AS genes were identified and characterized in wheat cultivar Xiaoyan 6. Our study provides a comprehensive view of AS in the wheat cultivar Xiaoyan 6 and provides new insights into the complexity of AS in wheat. The data generated in this study provides a foundation for further studies of seed development in wheat.