Endometritis is among the most common bovine uterine diseases. It may cause infertility and affect the sustenance and progress of the cattle industry. In this study, a novel metabolomics technique based on ultra-performance liquid chromatography/ quadrupole time-of-flight mass spectrometry was used to compare the uterine secretion metabolomics of healthy cows and those with clinical endometritis, classified based on clinical symptoms. Univariate and multivariate statistical analyses identified significant differences between groups. Compared with healthy uterine secretion samples, coumaric acid, benzoic acid, and equol were downregulated in the clinical endometritis samples. However, L-phenylalanine, glutamine, succinic acid, linoleate, arachidonic acid, and other metabolites were significantly upregulated, revealing significant variations between healthy cows and those with endometritis (p < 0.05). This metabolomics approach may provide a more in-depth understanding of the pathobiology of endometritis and a theoretical framework for the diagnosis and treatment of bovine endometritis.