In practical missions, quadrotor drones frequently face the challenge of navigating through multiple predetermined waypoints in cluttered environments where the sequence of the waypoints is not specified. This study presents a comprehensive multi-waypoint motion planning framework for quadrotor drones, comprising multi-waypoint trajectory planning and waypoint sequencing. To generate a trajectory that follows a specified sequence of waypoints, we integrate uniform B-spline curves with a bidirectional A* search to produce a safe, kinodynamically feasible initial trajectory. Subsequently, we model the optimization problem as a quadratically constrained quadratic program (QCQP) to enhance the trackability of the trajectory. Throughout this process, a replanning strategy is designed to ensure the traversal of multiple waypoints. To accurately determine the shortest flight time waypoint sequence, the fast marching (FM) method is utilized to efficiently establish the cost matrix between waypoints, ensuring consistency with the constraints and objectives of the planning method. Ant colony optimization (ACO) is then employed to solve this variant of the traveling salesman problem (TSP), yielding the sequence with the lowest temporal cost. The framework’s performance was validated in various complex simulated environments, demonstrating its efficacy as a robust solution for autonomous quadrotor drone navigation.