Staphylococcus aureus (S. aureus) is one of the dangerous pathogens involved in serious infections with high risk for morbidity and mortality. Development of effective vaccines against S. aureus strains is urgently needed, but successful vaccines are not available yet. In this study, we designed five types of multi-epitope vaccine constructs, targeting lipoproteins associated bacterial iron metabolism, which are IsdE, SstD, SirA, HtsA, and SitC. Using immunoinformatic approaches, we selected various sequences as potent B cell and T cell epitopes and constructed virtual vaccines with linkers and N-terminal adjuvants. The vaccine constructs were evaluated and compared with respect to their physicochemical and structural properties as well as immunologic and allergenic profiles. Immune simulation studies showed the vaccines would increase immune cell populations and antibody and cytokine responses. The vaccine constructs had similar physicochemical and immunological characteristics, while specific constructs showed distinct immunestimulatory properties. With a further investigation of the vaccine constructs on in vivo host testings, the newly designed S. aureus iron-regulated lipoprotein vaccines would help us to prevent S. aureus infection with greater efficacy and better safety.