The concept of the natural frequency is useful for understanding the characters of oscillating systems. However, when a circular cylinder floating horizontally on the water surface is heaving, due to the hydrodynamic forces, the system is not governed by the equation like that of the harmonic one. In this paper, in order to shed some lights on the more correct use of the concept of the natural frequency, a problem of the heaving circular cylinder is analyzed in the frequency domain. Previously, it was thought that the theory of Ursell (1949) could not be used to get the added mass and wave-making damping for short waves, however, they were obtained by applying an accurate collocation method to the theory in this study. Using the so developed numerical method, we found the added mass and wave-making damping of the circular cylinder for the entire range of the frequency. Then, the MCFR(Modulus of Complex Frequency Response) was used to locate the frequency corresponding to the local maximum of MCFR and we define it as the natural frequency. Comparing our results with the previous investigation, we found that the pressure distribution on the cylinder gets close asymptotically to that of a cylinder in infinite fluid OR close to that of the cylinder, that the approximation of the natural frequency by Lee (2008) is different from our new value only by 0.64%, and that the approximation of the heaving system by an equivalent damped harmonic oscillation is not proper by the reason that is clearly shown from the comparison of the shape of the corresponding MCFRs.