Taiwan is located along the boundary of the Eurasian and the Philippine Sea plates and experiences tens of thousands of earthquakes each year. Based on historical records, Taiwan has had several earthquakes of magnitude greater than 7.0. Notable and deadly quakes occurred in 1906 (Meishan Earthquake), 1935 (Hsinchu-Taichung Earthquake), and 1999 (Chi-Chi Earthquake). Statistically, Taiwan has had a major earthquake every 30–60 years. Therefore, earthquake museums are needed for long-term earthquake education and geoheritage exhibitions. Earthquake museums highlight disaster risks and preparedness information. The purpose of preserving earthquake remains is to educate visitors about Taiwan’s natural disasters and provide a memorable experience that inspires earthquake preparedness. The Chushan trench across the Chelungpu fault is a good example of Chi-Chi Earthquake rupture. This trench has recorded the five most important earthquake events on the Chelungpu fault. Although the Chelungpu Fault Preservation Park (CFPP) has worked to preserve these earthquake remains, they have been threatened due to seepage over the years. The aim of this paper is to analyze trench seepage and explore the development of an anti-seepage model, to provide a reference for the preservation of earthquake remains and museum development worldwide.