The Santo Niño Church in Bohol Island was partially damaged in the Bohol Earthquake in October 2013. In this study, we investigated the structural property of the Santo Niño Church to understand the vibration characteristics of Philippine masonry constructions by checking the main damage and conducting measurement surveys and microtremor measurement on the structure and ground. The major findings of this study can be summarized as follows: (a) Collapsed walls, peeling wall stone, corner deformation, and collapsed ceiling were the main damages that were observed. The collapsed wall was measured, and the make-up and material thickness of the wall was verified. (b) By performing microtremor measurements on the walls, the vibration property of the church, such as the natural frequency and vibration mode of the longest wall A was clarified. The 1st natural frequency of the longest wall A is the lowest.