MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs (ncRNAs) that widely regulate gene expression at the post-transcriptional level. Throughout the stages of miRNA biogenesis, from the production of primary transcripts to the processing into precursors and finally mature forms, various nucleotide modifications occur. These modifications involve the enzymatic generation of other types of nucleotides based on the four classical ribonucleotides, or the template-independent addition of nucleotides to the ends of RNA molecules. This review summarizes the common types of nucleotide modifications during miRNA biogenesis, including methylation, terminal tailing, nucleotide editing, oxidation, and phosphorylation. Nucleotide modifications can influence the stability and processing efficiency of miRNAs at different stages, and modifications in mature miRNAs can affect their target gene range or alter the strength of their inhibitory effects on target genes. Nucleotide modifications of miRNAs are closely associated with various physiological and pathological processes in cells and can serve as molecular markers for clinical disease diagnosis or therapeutic targets, offering broad clinical application prospects.