Poria cocos is an edible fungus used as a health product and traditional Chinese medicinal preparation. Nevertheless, little is known about its nutrients. In this study, ultra‐high performance liquid chromatography coupled with triple‐quadrupole linear ion‐trap tandem mass spectrometry was conducted to quantify nucleosides, nucleobases, and amino acids in 32 batches of Poria cocos samples collected from Anhui, Sichuan, Hubei, Hunan, and Guizhou. Subsequently, the linearity, precision, repeatability, stability, and recovery of our methods were validated. Samples from different regions were clearly separated by partial least squares discriminant analysis and cluster analysis. Our results suggested that Poria cocos samples from different geographical environments differed in nucleosides, nucleobases, and amino acids. The plot of variable importance for projection disclosed differential compositions of L‐Leucine, Uridine, L‐Asparagine, L‐Glutamine, L‐phenylalanine, L‐Ornithine monohydrochloride, L‐Hydroxyproline, Taurine, and Inosine in Poria cocos from five regions. We found the highest content of total analytes, total amino acids, and total non‐essential amino acids in Poria cocos from Anhui, total essential amino acids in the Sichuan samples, and total nucleosides in the Hunan samples. Overall, we determined the content of Poria cocos‐derived nucleosides, nucleobases, and amino acids, providing the foothold for further chemical mining and use of Poria cocos.