This dataset contains the raw gas chromatography–mass spectrometry (GC–MS) data of fecal metabolites associated with the clinical trial "Efficacy of heat-treated postbiotic Lacticaseibacillus rhamnosus in patients with functional bowel disorders: a randomized, double-blind, placebo-controlled clinical trial." Fecal metabolites were extracted from 40 mg of each fecal sample in 1.2 mL of 75% methanol (v/v in water), dried under vacuum, and derivatized with methoxyamine hydrochloride in pyridine followed by N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA). A mixture of alkane standards and fluoranthene served as the retention index marker and internal standard, respectively. Analysis was performed on a Thermo Trace 1310 GC system coupled to a Thermo ISQ LT single quadrupole mass spectrometer equipped with an Agilent DB-5MS column (60 m × 0.25 mm, 0.25 µm film). Mass spectra were acquired in electron-impact ionization mode over m/z 35–650 at 5 spectra/s. Full instrumental and chromatographic parameters are described in the Materials and Methods section of the associated publication. The data are provided as .cdf format, one file per sample, together with a sample-metadata table linking each file to its treatment group (heat-treated postbiotic vs. placebo) and time point. Peak detection and metabolite annotation were carried out with, AMDIS, and MS-DIAL, with identifications matched against the NIST Mass Spectral Library (v2.0). Relative metabolite peak areas were total-sum normalized per sample and auto-scaled (mean-centered, unit variance) prior to multivariate analysis. These data are shared to support reproducibility and reanalysis of the metabolomic findings reported in the study. Researchers reusing this dataset are requested to cite the associated publication.