Ionic liquids are popular in diverse scientific applications because of their unique physicochemical properties. The physicochemical properties of ionic liquids can be "tuned" by the modification of their structural moieties. Understanding of structure-property relationship is important if one wants to introduce a desired property in ionic liquid for a specific application. The initial part of this thesis will discuss the understanding of structure-property relationship of dicationic ionic liquids. Ionic liquids with high thermal stability are useful in many applications from simple solvents for high temperature reactions to high vacuum lubricants for space applications. This thesis presents the design, synthesis, and characterization of different thermally stable dicationic ionic liquids. ILs with TGA thermal stabilities in the range of 330 to 467 °C and inverse gas chromatography stabilities up to 400 °C are reported. The thesis also provides an understanding of the thermal behavior of ionic liquids at higher temperatures. The first, in depth thermal decomposition study of dicationic ionic liquids by using electrospray ionization mass spectrometer is presented, and it discusses the mechanism of thermal degradation of ionic liquids and their degradation products at high temperatures. Two important applications of thermally stable ionic liquids, stationary phases for gas chromatography and solvents for high temperature reactions are discussed in this thesis. Applications of thermally stable dicationic ionic liquid gas chromatography stationary phases for the high temperature separation of high molecular weight compounds is presented. Applications of ionic liquid stationary phases in the separation of structural isomers of toxic environmental pollutants, compounds with different functional groups and polarities are reported. A fundamental investigation of the effect of structural modifications such as cations, linkage chains, and anions on the selectivities of ionic liquids is discussed. The last chapter of the thesis presents the application of thermally stable monocationic phosphonium ionic liquid as a solvent in a high temperature synthesis. The advantages of higher thermal stability and the catalytic properties of ionic liquid were utilized for the "rapid" deprotection of tert-butoxy amino acids and peptides at higher temperatures.