Compared to conventional MS and NMR techniques, high-performance chemical isotope labeling (CIL) LC-MS provides accurate relative quantification of many more metabolites in biological samples. However, to apply this technique for urine and fecal metabolomics studies of animal models, the entire workflow, including the preanalytical process, needs to be strictly controlled to avoid or minimize quantitative errors. In this study, we report our investigation of the effects of mouse urine and fecal sample collection methods on CIL LC-MS metabolome analysis. Metabolic-cage collection and spot-sample collection of urine and feces were compared in a mouse model of CCl4-induced liver disease. 13C-/12C-dansylation LC-MS was used for quantitative profiling of the amine-/phenol-submetabolome changes. A total of 5026, 4963, 4238, and 4600 peak pairs or metabolites were detected from spot urine, spot feces, cage-collected urine, and cage-collected feces, respectively. It was found that samples collected using metabolic cages, widely used in low coverage metabolomics, could be contaminated with food as well as cross-specimen (urine in feces or feces in urine) to the extent that metabolomic comparison of different groups of mice could be seriously compromised in high-coverage metabolomics. In contrast, spot urine and spot feces could be collected without contamination and should be used in CIL LC-MS metabolomics.