This paper focuses on the autonomous motion control of 3-D underactuated overhead cranes in the presence of obstacles, and an “offline motion planning + online trajectory tracking” framework is developed. In the motion planner, to meet the balance between transfer time and energy consumption, the transfer mission is formulated as an energy-time hybrid optimal control problem. And a simple and conservative collision-avoidance condition is derived. To achieve fast and robust calculations, an iterative procedure that determines optimal terminal time based on the secant method is developed. Finally, to realize the high-precision trajectory tracking and fast residual sway suppression, a model predictive controller with a piecewise weighted matrix is designed. Numerical simulation demonstrates that the discussed framework is effective.