Cholestasis is characterized by obstruction of bile flow and can lead to serious liver injury. With sustained damage, cholestasis can progress to cholestatic liver fibrosis (CLF), and cirrhosis. Non-invasive, predictive, and reliable metabolites based on the early and progressive stages of CLF are urgently needed. Based on the 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-induced CLF mouse model, serum metabolic profiling via a time-series strategy with ultra-performance liquid chromatography-LTQ-Orbitrap-based metabolomics, combined with histological progression, was used to find CLF-specific metabolites, and explore their dynamic changes in progressive stages of CLF. Compared to those in the control group, DDC-induced groups showed a substantial elevation in cholestatic liver injury and fibrosis indices. Next, 21 differential serum metabolites were selected and identified between the normal (control) and DDC groups, and 12 of them were greatly altered over time. Among these, taurocholic acid, tauromuricholic acid, LysoPE (20:2), sulfoglycolithocholic acid, and taurohyodeoxycholic acid were associated with the progression of the hepatocyte injury index, alanine aminotransferase. More importantly, docosahexaenoic acid, arachidonic acid, proline, leucine, and linoleic acid were associated with the progression of liver fibrosis index, liver hydroxyproline. Moreover, the differential metabolites that were related to hepatocyte injury and liver fibrosis were further validated in DDC-induced mice at weeks 4 and 8. Overall, this work provides data on differential metabolites for the progressive pathology of CLF.