Micro aerial vehicles (MAVs), especially quadrotors, have been widely used in field applications, such as disaster response, field surveillance, and search‐and‐rescue. For accomplishing such missions in challenging environments, the capability of navigating with full autonomy while avoiding unexpected obstacles is the most crucial requirement. In this paper, we present a framework for online generating safe and dynamically feasible trajectories directly on the point cloud, which is the lowest‐level representation of range measurements and is applicable to different sensor types. We develop a quadrotor platform equipped with a three‐dimensional (3D) light detection and ranging (LiDAR) and an inertial measurement unit (IMU) for simultaneously estimating states of the vehicle and building point cloud maps of the environment. Based on the incrementally registered point clouds, we online generate and refine a flight corridor, which represents the free space that the trajectory of the quadrotor should lie in. We represent the trajectory as piecewise Bézier curves by using the Bernstein polynomial basis and formulate the trajectory generation problem as a convex program. By using Bézier curves, we can constrain the position and kinodynamics of the trajectory entirely within the flight corridor and given physical limits. The proposed approach is implemented to run onboard in real‐time and is integrated into an autonomous quadrotor platform. We demonstrate fully autonomous quadrotor flights in unknown, complex environments to validate the proposed method.