The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators for plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. To better understand the role of microRNA in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4°C revealed that the auxin signaling mutant, solitary root 1 ( slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRNA in wild-type and slr1 mutant roots using next-generation deep sequencing revealed 180 known and 86 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26nt-31nt small RNA population in slr1 compared with wild-type. Comparative analysis of microRNA expression shows differential expression of 13 miRNAs in slr1 compared with wild-type. Target gene expression analysis of one of the potential candidate miRNAs, miR169 revelaed the possible involvement of miR169- NF-YA module in the auxin-mediated cold stress response. Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRNA in auxin and cold responses.