Predicting tsunami hazards based on the tsunami source, propagation, runup patterns is critical to protect humans and property. Potential tsunami zone, as well as the historical tsunamis in 1983 and 1993, can be a threat to the east coast of South Korea. The Korea Meteorological Administration established a tsunami forecast warning system to reduce damage from tsunamis, but it does not consider tsunami amplification in the bay due to resonance. In this study, the Numerical model, Cornell Multi-grid Coupled Tsunami model, was used to investigate natural frequency in the bay due to coastal geometry. The study area is Yeongill bay in Pohang, southeast of South Korea, because this area is a natural bay and includes three harbors where resonance significantly occurs. This study generated a Gaussian-shaped tsunami, propagated it into the Yeongill bay, and compared numerical modeling results with data from tide gauge located in Yeongill bay during several storms through spectral analysis. It was found that both energies of tsunamis and storms were amplified at the same frequencies, and maximum tsunami wave height was amplified about 3.12 times. The results in this study can contribute to quantifying the amplification of tsunami heights in the bay.