The geothermal prospect located at Gunung Endut was investigated in 1980s based on reconnaissance surveys, primarily on geological and geochemical aspects. Then in 2006 a gravity measurement with 247 stations was carried out. However, due to the distribution of the gravity station was less than optimal, interpretation of gravity data was not suitable with the geological situation that support geothermal system. To ensure this, we have carried out a new gravity survey with 134 random stations distribution but remained concentrated on hot spring locations. Data from both measurements were processed by the same treatment starting from pre-processing with some standar corrections to obtain complete Bouguer anomaly, then continue by filtering process to separate regional and residual gravity anomaly using Butterworth filter in a wavenumber domain. Residual gravity anomaly map obtained by random position of stations is more resemble to the geological features developed in the prospect area. The contrast boundaries of the residual gravity anomaly value coincide with the fault-line structures recorded in the surface geological data. This result is better when compared with previous measurements. This study shows that there is a significant influence of the distribution pattern of the gravity stations which affects the conformity with the geological data. Based on the new interpretation result, the structural features in the prospect area are characterized by the complex fault structures that intersected each other mainly close to the surface manifestations. This intersection area is expected to be an enhanced permeability zone so that the hydrothermal fluid can flow to the surface. The interpretation of new gravity data combined with the results of geochemical analysis can be used for more understanding of the geothermal system beneath Gunung Endut prospect area.