Temperature has a severe impact on maize height. However, the mechanisms by which maize regulates height in response to heat have not been fully established. Here, we perform a genome-wide association study and identify one single nucleotide polymorphism (SNP) located in the maize MIR172C promoter strongly associated with temperature-dependent plant height. This SNP is selected during maize domestication from tropical to temperate zones. Molecular evidence shows that the G-to-A variation enhances the binding of PIF4 to the MIR172C, greatly represses MIR172C transcription. Phenotyping indicates that MIR172C is highly expressed in the meristem to promote internode elongation. miR172c represses its target IDS1 and activates the brassinosteroid (BR) pathway in a temperature-dependent manner. Under heat stress, miR172s regulate IDS1 predominantly by translational inhibition. This study identifies a natural variation modulating temperature-dependent maize height and elucidates the underlying mechanism. This finding reports a key locus for future breeding to enhance environmental adaptability in maize.