Owing to the randomness in the fracture flow system, the seepage system beneath a complex rock mass dam is inherently complex and highly uncertain, an investigation of the dam leakage by estimating the spatial distribution of the seepage field by conventional methods is quite difficult. In this paper, the entropy theory, as a relation between the definiteness and probability, is used to probabilistically analyze the characteristics of the seepage system in a complex rock mass dam. Based on the principle of maximum entropy, an equation for the vertical distribution of the seepage velocity in a dam borehole is derived. The achieved distribution is tested and compared with actual field data, and the results show good agreement. According to the entropy of flow velocity in boreholes, the rupture degree of a dam bedrock has been successfully estimated. Moreover, a new sampling scheme is presented. The sampling frequency has a negative correlation with the distance to the site of the minimum velocity, which is preferable to the traditional one. This paper demonstrates the significant advantage of applying the entropy theory for seepage velocity analysis in a complex rock mass dam.