This study aimed to evaluate the clinical value of the monocyte to high-density lipoprotein cholesterol ratio (MHR) and alkaline phosphatase-to-platelet ratio (APPR) in the diagnosis and prognosis of primary biliary cholangitis (PBC). Clinical and laboratory data were retrospectively collected and analyzed from 92 PBC patients, 92 patients with autoimmune hepatitis (AIH), 120 patients with chronic hepatitis B (CHB) and 124 healthy controls (HCs). We compared the levels of MHR and APPR among the groups with PBC, AIH, CHB and HCs, and analyzed the correlations between MHR and APPR with laboratory indices including aspartate aminotransferase platelet ratio index, fibrosis index based on 4 factors, and Mayo score in PBC. Receiver operating characteristic curves were used to analyze the diagnostic performance of MHR and APPR for PBC, AIH, and CHB, respectively. MHR and APPR were significantly increased in PBC group than that in AIH, CHB and HCs groups (each P < .05). MHR and APPR were significantly higher in Child class B|C than that in class A in PBC patients. (P < .01, P < .05, respectively). MHR and APPR were positively related to the Mayo score [R = 0.508 (P < .001), R = 0.295 (P = .008), respectively]. The area under the receiver operating characteristic curves of MHR and APPR in diagnosing PBC were 0.764 (95% confidence interval [CI]: 0.699–0.821, P < .001) and 0.952 (95% CI: 0.915–0.977, P < .001), respectively, and the area under the curve of the combination of both was 0.974 (95% CI: 0.941–0.991, P < .001). MHR and APPR may prove to be useful prognostic biomarkers for PBC, and the combination of MHR and APPR have some clinical diagnostic value of PBC.