The inefficient conversion of carbon dioxide (CO2) to methane often restricts the advancement of CO2 biomethanation technologies. This study explored the degrading performance, microbial community compositions, and functional gene abundance to examine the impact of zirconium metal-organic frameworks (Zr-MOFs) on the CO2 biomethanation process. The results showed that the maximum utilization rates of CO2 and H2 increased by 2.77 times and 2.36 times after the addition of Zr-MOFs, respectively, and the corresponding conversion rate of CO2 to methane also increased by 57.53%. Additionally, Zr-MOFs enhanced the COD removal efficiency and hydrolysis of tryptophan-like proteins and humic acid-like substances, resulting in more volatile organic compounds, such as tetradecane, 2-pentanone, and hexadecanoic acid. The analysis of microbial community structure revealed that the relative abundance of Methanothrix and Metanobacterium increased by 24.40% and 36.02% after the addition of Zr-MOFs, respectively. The methane metabolism revealed that Metanobacterium was a member of the same aceticlastic methanogenic pathway as Metanothrix, which encodes acetyl-CoA synthetase to catalyze the synthesis of acetyl-CoA from acetate, and Zr-MOFs also increased the relative abundance of genes that encode the enzyme responsible for converting intermediates to methane. Finally, Zr-MOFs improved the biogenesis and utilization of acetate and hydrogen (H2) by enhancing the activity of enzymes, thereby providing more nutrients for methanogenesis. This study provided thorough explanations for the application and improvement of Zr-MOFs in CO2 biomethanation technology.