Objective To explore the effects of combined artificial kidney on secondary hyperparathyroidism and intestinal microbiota in maintenance hemodialysis (MHD) patients. Methods A total of 40 patients who received MHD treatment at the Blood Purification Center of the Affiliated Hospital of Youjiang Medical University for Nationalities from December 2022 to November 2023 were selected as research subjects, and they were randomly divided into a hemodialysis (HD) group or an HD+hemoperfusion (HP) group, with 20 cases in each group. Calcium and phosphorus metabolism indicators, levels of fibroblast growth factor (FGF)-23 and Klotho protein, and intestinal microbiota colony counts were compared between the two groups before treatment and after 6 months of treatment. Results Before treatment, there was no statistically significant difference between the two groups in the serum levels of calcium, phosphorus, parathyroid hormone (PTH), FGF-23, or Klotho protein, or in the colony counts of intestinal Lactobacillus, Bifidobacterium, Enterococcus, or Escherichia coli (all P>0.05). After 6 months of treatment, the serum levels of calcium and Klotho protein and the colony counts of intestinal Lactobacillus and Bifidobacterium in the HD+HP group were higher than those in the HD group, while the serum levels of phosphorus, PTH, and FGF-23 and the colony counts of Enterococcus and Escherichia coli were lower than those in the HD group (all P<0.05). Conclusion The combined artificial kidney can significantly improve secondary hyperparathyroidism-related indicators (calcium-phosphorus metabolism, PTH, FGF-23/Klotho axis) and correct intestinal dysbiosis in MHD patients by synergistically removing uremic toxins. Its mechanism may be related to reducing toxin-induced damage to the parathyroid gland and intestinal mucosa.