The role of nucleic acid molecules has increased in biomedicine and material science. However, natural nucleic acid molecules display limitations in practical applications, such as unstable structures and a single-function design, necessitating functional modification. Modification can adjust the structure and chargeability of nucleic acids, enriching their chemical functionality and improving their performance while showing significant potential in the fields of biology and medicine. Current research mainly focuses on applying modified nucleic acids in a certain field and involves the type and mechanism of nucleic acid modification. This chapter addresses the complexity presented by the types, strategies, and application scenarios of nucleic acid modification. This review uses the nucleotide composition to summarize the current 155 nucleic acid modifications in terms of phosphate backbone, (deoxy)ribose, bases, and artificial nucleic acids (ANAs). These modifications mainly improve the eight nucleic acid functions, namely, gene expression regulation, target interaction enhancement, nucleic acid stability improvement, nucleic acid chain amplification termination, functional group linkage, fluorescent signal output, nucleic acid reducibility improvement, and as a photolytic agent. An appropriate strategy and direction were proposed to realize the reliable and extensive application of nucleic acid modification while establishing a connection between the structure and function. The synthesis, interaction mechanism, biological effect, and rational design of modified nucleic acids require further exploration in future research.