Although the coronavirus pandemic has ended, new variants of concern (VOCs) continue to emerge. Therefore, novel vaccines targeting VOCs are highly warranted. We initially constructed three recombinant baculovirus-vectored vaccines (AcHERV-COVID19S) carrying the spike genes of the SARS-CoV-2 prototype, Delta, and Omicron BA.1 variants. However, the SARS-CoV-2 spike gene alone could not provide protection against multiple VOCs. To develop a universal vaccine, we constructed a recombinant baculovirus-vectored vaccine (AcHERV-COVID19 OmiM) by introducing the M gene, which is conserved among VOCs, as a secondary cellular immune antigen in addition to the S gene. AcHERV-COVID19 OmiM could provide higher protection against SARS-CoV-2 variants (prototype, Delta, BA.5 and XBB.1) compared with that of AcHERV-COVID19S. The membrane protein of SARS-CoV-2 synergizes with the S gene, thereby enhancing both humoral and cellular immunity against VOCs. Although AcHERV-COVID19 OmiM may not provide sterile protection against new variants, it may help reduce symptoms and curb viral transmission.