Metabolomics analysis has developed rapidly in recent decades and has become a powerful tool to understand comprehensive metabolic changes in biological systems. In Parkinson’s disease (PD) research, great efforts have been made toward the discovery of novel biomarkers and biochemical pathways to improve diagnosis, prognosis, and therapy. With the recent achievements in metabolomics, the identification of multiple novel biomarkers for PD has been greatly improved. In this chapter, we outline a detailed metabolomics workflow including sample pretreatment, instrumental analysis, and data interpretation and summarize recent advances in technology and bioinformatics implemented in metabolomics studies. Based on the current metabolomic findings in PD research, this chapter covers the most promising metabolic biomarkers and pathway disturbances in PD and discusses the progress made toward translating these findings to clinical practice, emphasizing the potential importance of endogenous small molecular metabolites in disease research.