Methyltransferase VP39 is an important target for the treatment of monkeypox, and inhibition of VP39 can effectively suppresses the transcription and translation of early viral RNA. However, very few inhibitors have been designed against VP39 and other viral MTases. In this work, four inhibitors (SFG, TO507, TO427 and TO1119) were used to investigate the binding mechanism with VP39. Moreover, VP39 has different modes of existence, but we do not understand the interaction mechanism of the complex system formed by the inhibitors with different modes of VP39, so we performed 1000 ns molecular dynamics simulations of the complexes formed by four inhibitors with VP39 in mode 1 and mode 2, and performed energy calculation and conformational analysis. The results of binding free energy showed that in the inhibitors-VP39 (mode 1) systems, TO507 and TO427 had a strong inhibitory effect on VP39, and residues ASP95, ARG97, PHE115 and VAL139 played important roles in the binding process of all four systems. Surprisingly, in the inhibitors-VP39 (mode 2) systems, four inhibitors underwent a large conformational change, with the amino acid moieties of the inhibitors undergoing a nearly 90° folding. And this change reduced the inhibitory effect of the inhibitors on VP39. In addition, the inhibitor TO507 also had a good inhibition effect on nsp14 of SARS-CoV-2 and NS5 of Zika virus. Therefore, this study suggests new ideas for the design and improvement of pan-MTase inhibitors, which are important for the treatment of pandemic infectious diseases, such as monkeypox and SARS-CoV-2.