Spacecraft are now required to possess all-weather, zero-window, and support-independent launch capabilities. Consequently, research on spacecraft targeting must continue to focus on improving convenience and efficiency. In this paper, a spacecraft targeting method based on point cloud alignment is proposed. Firstly, external Triple Self-targeting Inertial Measurement Units are utilized to complete self-targeting. Secondly, the 3D point cloud of the spacecraft is obtained by binocular imaging technology, and an attitude transformation matrix is obtained by aligning the measured point cloud with the standard point cloud. Finally, the installation relationships between the binocular camera and the Triple Self-targeting Inertial Measurement Units, as well as between the guidance system and the spacecraft body, are determined. Combining these installation relationships with the attitude transformation matrix, the targeting results from the Triple Self-targeting Inertial Measurement Units are transferred to the spacecraft guidance system. In the simulation experiment, the maximum standard deviation of the three directions after multiple targetings is 9′9″, which can meet the requirements of spacecraft targeting. The method proposed in this paper fully retains the self-targeting advantages of the Triple Self-targeting Inertial Measurement Units without external support, while making spacecraft targeting more flexible and rapid. If applied to actual equipment, it will effectively enhance the adaptability of spacecraft equipment to environments.