Monascus azaphilones pigments (MonAzPs) produced by microbial fermentation are widely used as food chemicals for coloring and supplying beneficial biological attributes. In this study, a fermentation perturbation strategy was implemented by separately adding different amino acids, and detecting the intracellular metabolome via UHPLC-Q-Orbitrap HRMS. With the aid of weighted gene co-expression network analysis, two metabolic intermediates, fumarate and malate, involved in the tricarboxylic acid cycle, were identified as the hub metabolites. Moreover, exogenous addition of fumarate or malate significantly promoted red pigment production, and reduced orange/yellow pigment production. The importance of the tricarboxylic acid cycle was further emphasized by detecting intracellular levels of ATP, NAD(P)H, and expression of oxidoreductase-coding genes located in the MonAzPs synthetic gene cluster, suggesting a considerable effect of the energy supply on MonAzPs synthesis. Collectively, metabolomics is a powerful approach to position the crucial metabolic regulatory factors, and facilitate the development of engineering strategies for targeted regulation, lower trial-and-error cost, and advance safe and controllable processes for fermented food chemistry industries.