Anther dehiscence controls optimal interaction between pollen and stigma, thereby determining the successful sexual reproduction. The regulators or mechanisms of this process remain elusive. Here, two CRISPR/Cas9 mutants of a rice exocyst subunit gene SEC3A, sec3a-1 and sec3a-2, showed anther indehiscence at anthesis and male sterility at maturity. Pollen viability and germination in the mutants were partly defective, whereas their female gametes undergone a normal development. Hybrid or self-pollinated seeds could be produced by artificial pollination, suggesting potential use of a weak sec3a mutant as a female line during hybrid breeding. SEC3A is widely expressed in various tissues, including anther walls. Further results showed an excessive IAA accumulation and no endothecium lignification in sec3a-1/2 anthers. Our findings suggest that SEC3A appears to regulate anther dehiscence by modulating auxin signaling, providing insights into regulation of anther dehiscence and function of exocyst in plants.