Autophagy degrades cellular components during senescence, starvation, and stress. High-temperature (HT) stress can inhibit microsporogenesis, but the involvement of autophagy in HT injury is unknown. Here we show that Arabidopsis autophagy-defective (atg) mutants are hypersensitive to HT stress during microsporogenesis but not during seedling growth. Fertility was normal at 23 °C, but sporophytic male sterility occurred at 30 °C. At 30 °C, wild-type developing anthers showed increased vacuolization in tapetum and lipophagy in microspores. The atg5-1 mutant did not show these autophagic phenomena, but instead showed irregularly enlarged vacuoles and subsequent shrinkage, and failure of the tapetum to degenerate completely. HT specifically upregulated ATG8 in the developing anther, but not in seedlings, and reduced MYB80 signaling in the anther, which is required for the regulation of tapetal programmed cell death to promote microspore maturation. Interestingly, inhibition of auxin activated the ATG8 signal in seedlings at both 23 and 30 °C. These results, combined with our previous observation of anther-specific auxin depletion caused by HT, suggest that autophagy mitigates HT injury to microsporogenesis.