Lonicerae japonicae Flos (LJF) possesses a good anti-respiratory syncytial virus (RSV) effect. However, the material basis of LJF in treating RSV is still unclear. In this study, a sensitive and accurate quantitative method based on UHPLC-QQQ MS was established and validated for the simultaneous determination of the 15 ingredients from LJF in RSV-infected mice plasma. Multiple reaction monitoring was performed for quantification of the standards and of the internal standard in plasma. All the calibration curves show good linear regression within the linear range (r > 0.9918). The method validation results, including specificity, linearity, accuracy, precision, extraction recovery, matrix effect, and stability of 15 ingredients, are all within the current acceptance criteria. This established method was successfully applied to the pharmacokinetic study of 15 compounds from LJF. Furthermore, the repair rate of lung index and the improvement rate of IFN-γ and IL-6 improved after administration of the LJF, indicating that LJF possessed a positive effect on the treatment of RSV infection. Finally, by combining Spearman and Grey relation analysis, isochlorogenic acid B, isochlorogenic acid C, secoxyloganin, chlorogenic acid, and loganic acid are speculated to be the main effective ingredients of LJF in treating RSV. This study lays the foundation for attempts to reveal the mechanisms of the anti-RSV effect of LJF.