3-Methylnonane is primarily used as a reference compound in gas chromatography and mass spectrometry for the analysis of hydrocarbon mixtures. It serves as a standard for identifying and quantifying similar hydrocarbons in petroleum products and environmental samples. Additionally, it is utilized in research and development for studying the properties and behavior of branched alkanes in various chemical processes. Its application extends to the formulation of specialty fuels and lubricants, where its structural characteristics contribute to desired performance properties.