This paper presents a method for accurately estimating the natural frequencies of bridges by simultaneously measuring the acceleration vibration data of vehicles and bridges and applying modal analysis theory. Vibration sensors synchronized with GPS timing were installed on both vehicles and bridges, achieving stable and high-precision time synchronization. This enabled the computation of the bridge’s Frequency Response Functions (FRFs) for each mode, leading to a refined estimation of natural frequencies. The validity of the theory was confirmed through numerical simulations and experimental tests. The simulations confirmed its effectiveness, and similar trends were observed in actual bridge measurements. Consequently, this method significantly enhances the feasibility of bridge health monitoring systems. The proposed method is suitable for road bridges with spans ranging from short- to medium-span length, where the vehicle is capable of exciting the bridge.