Eglinton (1996) firstly performed the Compound-Specific Radiocarbon Analysis (CSRA) in marine sediments, providing a new approach to understanding the organic carbon source. The applications of CSRA technique were developed rapidly and widely used in oceanography, biogeochemistry and paleoclimatology. However, because of the extremely low amount and interference with complex substrates, mostly source-specific biomarkers were hard to be separated from environmental matrix samples. Therefore, how to harvest pure biomarkers, from complex natural sample matrixes, has been the limitation of CSRA technique, especially for ultra-small size CSRA. Recently, various preparative chromatography techniques have been carried out to improve the purity and recovery efficiency of the target compounds. This paper aimed to introduce the techniques and applications of CSRA for common source-specific biomarkers in the natural environment.