This paper reviews the progress of traditional carbon and oxygen isotope research of lacustrine carbonate and emerging clumped isotope research in recent years, summarizes their influencing mechanisms and applications in geological research, and discusses the problems in existing research. The oxygen isotope composition of lacustrine carbonates is less affected by temperature, which is mainly related to the evaporation and precipitation of lake water. The carbon isotope composition is jointly controlled by the evaporation and salinization of lake water and the interaction between organic matter and inorganic matter. The clumped isotope is only affected by the single factor of temperature and is a good carbonate thermometer. The paper points out two major directions for the study of carbon and oxygen isotopes of lacustrine carbonate: one is to solve the problems existing in the theoretical study of clumped isotopes, especially the resetting mechanism of clumped isotope temperature during burial; and the other is to combine traditional carbon and oxygen isotopes with emerging clumped isotope for comprehensive analysis of multi-index geochemistry, which can effectively resolve their limitation in geology research.