Trajectory planning for quadrotors in cluttered environments has been challenging in recent years. While many trajectory planning frameworks have been successful, there still exists potential for improvements, particularly in enhancing the speed of generating efficient trajectories. In this paper, we present a novel hierarchical trajectory planning framework to reduce computational time and memory usage called MINER-RRT*, which consists of two main components. First, we propose a sampling-based path planning method boosted by neural networks, where the predicted heuristic region accelerates the convergence of rapidly-exploring random trees. Second, we utilize the optimal conditions derived from the quadrotor's differential flatness properties to construct polynomial trajectories that minimize control effort in multiple stages. Extensive simulation and real-world experimental results demonstrate that, compared to several state-of-the-art (SOTA) approaches, our method can generate high-quality trajectories with better performance in 3D cluttered environments.