Developing and optimizing an x-ray scatter control and reduction technique is one of the major challenges for cone beam computed tomography (CBCT) because CBCT will be much less immune to scatter than fan-beam CT. X-ray scatter reduces image contrast, increases image noise and introduces reconstruction error into CBCT. To reduce scatter interference, a practical algorithm that is based upon the beam stop array technique and image sequence processing has been developed on a flat panel detector-based CBCT prototype scanner. This paper presents a beam stop array-based scatter correction algorithm and the evaluation results through phantom studies. The results indicate that the beam stop array-based scatter correction algorithm is practical and effective to reduce and correct x-ray scatter for a CBCT imaging task.