Nuclear magnetic resonance (NMR) spectroscopy has been used to obtain the profile of soluble metabolites on fungus. To enhance the ergothioneine content in Pleurotus citrinopileatus mycelium, amino acid precursors were used for submerged fermentation. The study aimed to analyze the metabolites of high-ergothioneine and regular P. citrinopileatus mycelia (HEPM and RPM) and P. citrinopileatus basidiomata (PCB) using NMR spectroscopy. Principal component analysis (PCA) was applied to differentiate and to describe the differences among three sets of metabolites. The results showed that 55 water-soluble metabolites of PCB, HEPM, and RPM were identified and classified into five groups including amino acids, carbohydrates, organic acids, purines and pyrimidines, and others. Contents of total soluble metabolites were in descending order as follows: PCB (135 mg/g) > HEPM (58 mg/g) > RPM (44 mg/g). The score plot and loading plot separated using PCA showed that the first two components were responsible for R2X = 97.1% and the variance [R2X(1) = 74% for principal component PC1 and R2X(2) = 23.1% for PC2]. A metabolic pathway map of P. citrinopileatus mycelium was established and the differences in the metabolites of RPM and HEPM with precursors added were illuminated.