Low-altitude flight in mountainous terrains is a difficult flight task applied in both military and civilian fields. The helicopter has to maintain low altitude to realize search and rescue, reconnaissance, penetration, and strike operations. It contains complex environment perception, multilevel decision making, and multi-objective flight control; thus, flight is currently mainly conducted by human pilots. In this work, a control framework is implemented to realize autonomous flight for unmanned helicopter operations in an unknown mountainous environment. The identification of targets and threats is introduced using a deep neural network. A 3D vector field histogram method is adopted for local terrain avoidance based on airborne Lidar sensors. In particular, we propose an intuitive direct-viewing method to judge and change the visibilities of the helicopter. On this basis, a finite state machine is built for decision making of the autonomous flight. A highly realistic simulation environment is established to verify the proposed control framework. The simulation results demonstrate that the helicopter can autonomously complete flight missions including a fast approach, threat avoidance, cover concealment, and circuitous flight operations similar to human pilots. The proposed control framework provides an effective solution for complex flight tasks and expands the flight control technologies for high-level unmanned helicopter operations.