Respiratory syncytial virus (RSV) infection is a global health concern that poses a significant threat to children under the age of five. Yet vaccine development has been hindered by historical safety concerns, including vaccine-associated enhanced respiratory disease (VAERD). To address these challenges, we rationally engineered a soluble, stable, and deimmunized flagellin-derived adjuvant (FIC) to activated mucosal immunity, which plays a critical role in protecting against respiratory diseases and is considered safe for children. In mouse models, FIC adjuvanted RSV prefusion F (preF) vaccines elicited a Th1-biased immune response, characterized by elevated expression levels of IFN-γ, IL-2, and TNF-α and robust pre-F-specific humoral, cellular, and mucosal immunity, while minimizing flagellin-associated immunogenicity. Further, a sequential immunization regimen incorporating FIC significantly enhanced protection against both upper and lower respiratory tract RSV challenges. Notably, intranasal sequential immunization enhanced antigen-specific cytokine production from splenocytes, thereby optimizing the vaccine's efficacy against RSV. These findings indicated that structure-guided adjuvant optimization combined with mucosal prime-boost strategies can overcome historical barriers in RSV vaccinology, offering a promising pathway for respiratory pathogen vaccine development.