Potassium (K) has an important effect on the growth and development of plants. Banana contains higher K content than many other fruits, and its plant requires more K nutrient in soil. However, the soil in the banana-producing areas in China is generally deficient in K. Therefore, understanding the mechanism of banana K absorption may assist in providing effective strategy to solve this problem. This study used two banana varieties with contrasting K tolerance, ‘Guijiao No. 1’ (low-K tolerant), and ‘Brazilian banana’ (low-K sensitive)to investigate K absorption mechanisms in response to low-K stress through miRNA and mRNA sequencing analysis. Under low-K condition, ‘Guijiao No.1’ showed higher plant height, dry weight, tissue K content and ATPase activity. Analysis of transcription factors showed that they were mainly in the types or classes of MYB, AP-EREBP, bHLH, etc. The sequencing results showed that ‘Guijiao No. 1’ had 776 differentially expressed genes (DEGs) and 27 differentially expressed miRNAs (DEMs), and ‘Brazilian banana’ had 71 DEGs and 14 DEMs between normal and low K treatments. RT-qPCR results showed that all miRNAs and mRNAs showed similar expression patterns with RNA-Seq and transcriptome. miRNA regulatory network was constructed by integrated analysis of miRNA-mRNA data. miR160a was screened out as a key miRNA, and preliminary functional validation was performed. Arabidopsis overexpressing miR160a showed reduced tolerance to low K, and inhibited phenotypic traits such as shorter root length, and reduced K accumulation. The overexpressed miR160a had a targeting relationship with ARF10 and ARF16 in Arabidopsis. These results indicate that miR160a may regulate K absorption in bananas through the auxin pathway. This study provides a theoretical basis for further study on the molecular mechanism of banana response to low potassium stress.