Lagerstroemia × ‘Xiaoxiang Huaxiu’ (an F1 hybrid of Lagerstroemia speciosa and Lagerstroemia indica ‘Ebony Embers’) exhibits significant sterility. Cytological studies have revealed numerous abnormal chromosomal behaviors during the meiotic division of pollen mother cells in L. × ‘Xiaoxiang Huaxiu’. Transcriptome sequencing identified that LiDMC1 and LiASY1 were expressed at very low levels in ‘Xiaoxiang Huaxiu’. To further verify whether the abnormal expression of LiDMC1 and LiASY1 was the fundamental cause of sterility in ‘Xiaoxiang Huaxiu’, we cloned the full-length gene sequences of LiDMC1 and LiASY1 from ‘Ebony Embers’. Using VIGS (virus-induced gene silencing) technology, pTRV1 and pTRV2 gene silencing vectors were employed to silence LiDMC1 and LiASY1 in the paternal parent ‘Ebony Embers’. The results indicated that in the double-silenced lines of ‘Ebony Embers’, the cytoplasm sizes of different tetrads during the tetrad stage varied significantly. There was a notable proportion of polyads, binucleate cells with micronuclei, and pentads. Additionally, pollen diameter varied significantly, closely resembling the sterility observed in ‘Xiaoxiang Huaxiu’. Pollen viability in the double-silenced ‘Ebony Embers’ decreased by 22.8%. This study demonstrates that the low expression of LiDMC1 and LiASY1 leads to abnormal microspore development in ‘Ebony Embers’, and their low expression is the cause of sterility in ‘Xiaoxiang Huaxiu’.