An integral equation describing riding waves, i.e., small-scale perturbation waves superposed on unperturbed surface waves, in shallow water of finite depth was studied via explicit Hamiltonian formulation, and the water was regarded as ideal incompressible fluid of uniform density. The kinetic energy, density of the perturbed fluid motion was formulated with Hamiltonian canonical variables[1], elevation of the free surface and the velocity potential at the free surface. Then the variables were expanded to the first order at the free surface of unperturbed waves. An integal equation for velocity potential of perturbed waves on the unperturbed free surface was derived by conformal mapping and the Fourier transformation. The integral equation could replace the Hamiltonian canonical equations which are difficult to solve. An explicit expression of Lagrangian density function could be obtained by solving the integral equation. The method used in this paper provides a new path to study the Hamiltonian formulation of riding waves and wave interaction problems.