The vigorous collision between the Eurasian plate and Philippine Sea plate in Taiwan causes a series of imbricate fold and thrust belts to develop at the deformation front. The Chukou Fault (CKF), characterized by a thrust type fault, located in Chiayi County, southwest (SW) Taiwan, is a prominent boundary between the fold-thrust belts and the Western Coastal Plain. Most of the seismicity in SW Taiwan is associated with this fault and its neighboring fault systems. The seismotectonic structures in the CKF zone, especially in the east, are complex due to the interactions among fault systems with distinct slip motions. To gain better insights into the seismogenic characteristics in the CKF zone, we used 1661 microearthquakes recorded by a temporary dense broadband seismic network and the Central Weather Bureau Seismic Network (CWBSN) between 2003 and 2004 to investigate the physical properties of the crust in the CKF zone. A waveform cross-correlation technique was applied to 143086 pairs of waveform data to determine the relative differential travel time between the P- and S-waves. By combining both the absolute and relative differential travel time data, we were able to obtain a new 3-D crustal P-wave velocity structure and Vp/Vs ratios. This study suggests that by using both absolute and relative differential travel time data in tomographic inversion can obtain precise 3-D velocity images and also gain better correlation between seismic events and fault structures, which is crucial for understanding the seismogenic process in our study area.