A novel analytical method for evaluating the buckling stability of the pier–cap–pile system under scour effect is proposed, and furthermore, the concept of rapid assessment of bridge buckling stability based on natural frequency is innovatively introduced in this paper. First, the total potential energy function of the bridge pier–cap–pile system is established, and the closed-form solution of structural system critical buckling load under scouring is solved according to the principle of stationary potential energy. Second, the sensitivity analyses of pier height, pier width, bending stiffness reduction in pier, pile slenderness ratio, pile bending stiffness reduction, m-value of soil and structural gravity to the buckling load are carried out. On this basis, 60 sets of sensitive parameter sample combinations are extracted by the Latin Hypercube Sampling algorithm, and a proxy model relating the critical buckling load to scour depth and the sensitive parameters are then developed using the McQuarter global optimization algorithm. Finally, the regression relationship model between the critical buckling load and the natural frequency is formed by combining the proxy model and the existing relationship between the scour depth and the first-order natural frequency. The feasibility of the proposed assessment method is demonstrated by the finite element method using a bridge case study, which provides an insight and a new means of quantitatively evaluating the safety of bridges under scour effect.