The emergence of SARS-CoV-2 variants poses enormous challenges to the prevention and control of COVID-19 with alterations in antigenicity, transmissibility and pathogenicity. The rapid evolution of RNA viruses could be caused by high mutation frequencies during replication, arising by replication errors, intergenomic recombination or even host deaminases. We sought to understand whether host deaminases are involved in SARS-CoV-2 mutation, and how they orchestrate host deaminases to trigger this process. Herein, we provided the experimental evidence that APOBEC and ADAR deaminases act as the driving forces for SARS-CoV-2 mutagenesis. Mechanistically, SARS-CoV-2 nucleocapsid (N) protein, which is responsible for packaging viral genomic RNA, complexes with host deaminases to facilitate viral RNA mutation. Moreover, N protein employs deaminases-involved condensates to further promote viral RNA mutation. Mutant N protein with F17A substitution, defective in entry of deaminases-involved RNA granules, leads to the decreased mutation of viral RNA, confirming the function of N protein-deaminase condensates on RNA editing. Our study sheds light on the novel mechanism of SARS-CoV-2 mutation during host-virus arms race.