ABSTRACTSalt‐alkali stress is one of the most widespread and devastating abiotic stress. Alternative splicing is a response pathway to such stress. However, the role of microexons in response to salt‐alkali stress in soybean remains obscure. In this study, we identified microexons related to salt‐alkali stress. We focused on analyzing the conserved sequence patterns of 27–30 bp microexons, and consistently observed conserved GT and AG sequences at the 5′ and 3′ ends of these microexons. Additionally, we found that the AP2 protein domain had the most abundant microexons. Interestingly, the majority of microexons in the AP2 transcription factor were 9 bp in length, encoding a conserved valine (V), tyrosine (Y), or leucine (L), suggesting their indispensable role. Furthermore, we cloned two transcripts of three AP2 genes with and without the salt‐alkali stress‐induced microexon and generated stable transgenic soybeans. Surprisingly, we discovered that the depletion of microexons in the AP2 gene enhances salt‐alkali resistance. Collectively, this characterization of microexon suggests a new scenario explaining soybean salt‐alkali stress resistance.