The invention relates to a nucleic acid reaction theory analysis method for nucleic acid single base changes. The method comprises the steps of: (1) calculating standard enthalpy change amount delta rH and standard entropy change amount delta rS of a complementary reaction and a mismatch reaction; (2) exhaustively calculating enthalpy change amount delta delta H and entropy change amount delta delta S of all single base changes, so as to obtain an enthalpy change amount and entropy change amount data table of the nucleic acid single base changes; and (3) obtaining enthalpy change and entropy change data of any single base change by looking up the data table, and meanwhile, calculating free reaction energy change amount delta delta G caused by the single base changes under any temperature and salinity, thereby instructing a nucleic acid reaction design. According to the method, the table is easy to look up; the method is simple to use; the method can be used in any nucleic acid reaction theory analysis that relates to the single base changes; and the method has high potential in promoting single base change detection probe design and theory analysis and design in other nucleic acid reaction fields.