Giant pandas represent one of the most endangered species worldwide, and their reproductive capacity is extremely low. They have a relatively long gestational period, mainly because embryo implantation is delayed. Giant panda cubs comprise only a small proportion of the mother's body weight, making it difficult to determine whether a giant panda is pregnant. Timely determination of pregnancy contributes to the efficient breeding and management of giant pandas. Meanwhile, metabolomics studies the metabolic composition of biological samples, which can reflect metabolic functions in cells, tissues, and organisms. This work explored the urinary metabolites of giant pandas during pregnancy. A sample of 8 female pandas was selected. Differences in metabolite levels in giant panda urine samples were analyzed via ultrahigh-performance liquid chromatography/mass spectrometry comparing pregnancy to anoestrus. Pattern recognition techniques, including partial least squares-discriminant analysis and orthogonal partial least squares-discriminant analysis, were used to analyze multiple parameters of the data. Compared with the results during anoestrus, multivariate statistical analysis of results obtained from the same pandas being pregnant identified 16 differential metabolites in the positive-ion mode and 43 differential metabolites in the negative-ion mode. The levels of tryptophan, choline, kynurenic acid, uric acid, indole-3-acetaldehyde, taurine, and betaine were higher in samples during pregnancy, whereas those of xanthurenic acid and S-adenosylhomocysteine were lower. Amino acid metabolism, lipid metabolism, and organic acid production differed significantly between anoestrus and pregnancy. Our results provide new insights into metabolic changes in the urine of giant pandas during pregnancy, and the differential levels of metabolites in urine provide a basis for determining pregnancy in giant pandas. Understanding these metabolic changes could be helpful for managing pregnant pandas to provide proper nutrients to their fetuses.