The invention relates to a hydraulic tunnel structure spanning a large-scale active fault zone and belongs to the technical field of water conservancy and hydropower application. According to the technical scheme, the hydraulic tunnel structure comprises an active fault spanning section, a buried type steel penstock section with two connected ends and an overhaul tunnel communicated with the active fault spanning section in the longitudinal direction of a tunnel, a combined type lining structure is adopted in the active fault spanning section, the active fault spanning section is composed of an outer layer structure and an inner layer structure in the radial direction of the tunnel, the outer layer structure comprises a one-stage annular support and a one-stage annular lining on the outer side in the radial direction, the one-stage annular support and the one-stage annular lining are of reinforced concrete lining structures, and the inner layer structure comprises a combined lining structure with steel pipes and corrugate telescopic joints, wherein the steel pipes and the corrugate telescopic joints are connected in series alternatively. The hydraulic tunnel structure spanning the large-scale active fault zone is safe and convenient to construct, has the good seismic capacity and the capacity for resisting large-scale fault creep diastrophism damage and is high in safety.