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Male sterility caused by long‐term high‐temperature (HT) stress occurs widely in crops. MicroRNAs (miRNAs), a class of endogenous non‐coding small RNAs, play an important role in the plant response to various abiotic stresses. To dissect the working principle of miRNAs in male sterility under HT stress in cotton, a total of 112 known miRNAs, 270 novel miRNAs and 347 target genes were identified from anthers of HT‐insensitive (84021) and HT‐sensitive (H05) cotton cultivars under normal‐temperature and HT conditions through small RNA and degradome sequencing. Quantitative reverse transcriptase‐polymerase chain reaction and 5′‐RNA ligase‐mediated rapid amplification of cDNA ends experiments were used to validate the sequencing data. The results show that miR156 was suppressed by HT stress in both 84021 and H05; miR160 was suppressed in 84021 but induced in H05. Correspondingly …